This is the TL,DR section, a summary and the gist of what you need to know including some very basic examples.

Single recognizable terms are valuable in quick, clean, and effective communication. Comms can get cloudy and fuzzy, making dispersing information not only inconvenient but, also a lethal liability.

Ex. of some useful terms/calls to initiate certain procedures or set certain conditions:

GENERAL QUARTERS: Everyone moves to battlestations and begins Combat/Damage Control Procedures.
LIBERTY CALL: Set in port and gives everyone free time to go AFK like using the head or getting tea NOT WHILE UNDERWAY, POINT, I still blame that whole ordeal on you >:( or complete random sub-board duties they don't usually have time for.
MUSTER AWAY TEAM AT (SPACE): All designated Away Team members are to report to (space) to prepare for an away mission.

Common procedures are incredibly useful for getting things done or for emergency operations, having set procedures for things like Combat, Repair, Inventory Managing, etc. is necessary for efficient completion of missions and accomplishing objectives.

Ex. of some useful procedures:

GENERAL QUARTERS: ALL HANDS are to acquire diving gear and welding torches, ALL security personnel report to the armory to gather weaponry and ammunition to repel intruders, ALL Engineering personnel report to their designated spaces to begin Damage Control procedures, ALL Medical Personnel report to medical, gather emergency supplies, then disperse to central locations.
LOW OXYGEN CONDITIONS: ALL HANDS are to acquire oxygen masks/diving gear, ALL Medical personnel are to prepare low oxygen treatments, ALL Engineering personnel are to prioritize repairs to oxygen generators and related equipment.

Organized crew structure is important to operating your vessel effectively, not just in designating roles like; Captain, Security, Medical, Mechanic, Engineer, but also additional or particular roles and responsibilities.

Ex. You have a large submarine with multiple Mechanics:
1 Mechanic is Mechanical Officer (MECHO) and reports to the Chief Engineer (CHENG) about status of ongoing mechanical activities.
1 Mechanic is Hull Repair Lead, taking control of all Hull repair activities both internal and external.
1 Mechanic is Crafting Manager, taking control of all crafting activities aboard.

The chain connects the ship to it's anchor, and the anchor keeps the ship still in rough conditions. It is important to have a clearly defined and strong Chain of Command (COC). Obviously, the Captain is at the top. I have created a handy, very simple chart as a basic idea of what the Chain of Command for my own crew is.



This chart breaks the crew down into 3 Departments which have their own responsibilities.
COMMAND AND SECURITY (C&S) Control the submarine's navigation and weapon systems. Maintain physical security of the submarine both internally and externally. Away Team (A-TEAM) Missions are overseen by C&S Personnel.
ENGINEERING (ENG) Control the submarine's power plant, crafting, and hull integrity. Maintain the capability of the submarine to function on a basic level, as well as the hull to prevent unintended sinking.
MEDICAL (MED) Control the submarine's medical and research systems as well as the plants if necessary. Maintain the health and well-being of the crew.

How this breaks down is the Commanding Office(CO) has overall command.
Executive Officer (XO) reports directly to the CO.
Chief Engineer (CHENG) reports directly to the CO.
Mechanical Engineers (MECH) and Electrical Engineers (ELEC) report directly to CHENG.
Gunnery Team (WEPS) reports directly to the XO.
Away Team (A-TEAM) Directly reports to the XO.

With a smaller crew this chart may not be necessary but it does indicate specific personnel who might have more experience or knowledge. I.e. Engineering personnel should go to CHENG for engineering wisdom as opposed to the CO.

This also highlights that while the CO has overall command, they can not do everything.

Communication is the Be All, End All when it comes to running a crew. When communication fails, the operation fails, the crew fails, and often with lethal consequences.

In order to minimize issues with the transmission/receiving of information your comms must be:

• Clear
  
• Concise

Note: This doesn't mean you only have to speak like this, if anything these are for tense moments and emergency situations, like fighting a Hammerhead swarm, or a major hull breach, or away missions.

CLARITY: The quality of being coherent and intelligible.
Your communication needs to be easily heard and understood, enunciating certain words that might become muddled over radio static is key. It's also why the NATO Phonetic Alphabet and why certain speaking rules were established.

"Hey you, it's me, message, over."
"It's me, response, over."

Note: Over isn't always completely necessary, but you're almost never wrong when using it.

Ex. Your away team is distant and suffering from some issues, they need some gear but can't currently afford to leave the area.

Captain (CO) "Away team, Command, sitrep (Situation Report, essentially asking current status.)
Away Team Lead "Away Team, we're aboard, suffered injuries, husk parasites dealt with, need more ammunition and medical supplies."
CO "Say again, need more what and medical supplies?"
ATL "Ammunition"
CO "Say again, comms are fuzzy."
ATL "Alpha-Mike-Mike-Oscar."
CO "Ammo aye, standby for resupply."
ATL "Standing by, out."

Cease Ex.

Words like "ammunition" can get lost since they've got a lot of syllables and also a specific one, the "sh" can get lost in static. "Alpha-Mike-Mike-Oscar" has clearly defined tones and pronunciation that it can shine through in hazy radio static.

CONCISE: Giving a lot of information clearly and in a few words; brief but comprehensive. Your communication must be brief and give key details to maintain overall awareness of what's happening without taking too much time on the net.

Ex. The submarine is engaged in combat with a massive swarm of Mudraptors, GQ has been called, hull is damage and breaches abound. Cheng has mustered the Hull Repair team in preparation for external hull repairs but the fighting is still going.

Chief Engineer (CHENG) "Captain, CHENG, Repair Team is standing by for EVA, over (Extra vehicular Activity, leaving the sub)
Captain (CO) "Cap, negative, swarm is still active. disperse team for internal repairs, re-muster once secured from GQ."
CHENG "Affirm, dispersing crew about the ship, out."

Cease Ex.

Notifying the captain that your team is ready to make repairs while they're dealing with another major issue is important to maintain awareness, but you don't want to divert too much attention, nor do you want to overshadow other people like the weapons team.

Another prime example is sub-wide announcements or calls for All Hands.

Ex. Your sub is approaching a Moloch, most of the crew is fulfilling standard duties. The moloch begins approaching, ready to introduce you to the cold, highly pressurized, and dark alien depths.

CO "GENERAL QUARTERS, GENERAL QUARTERS, ALL HANDS MAN YOUR BATTLESTATIONS, PREPARE THE SHIP FOR COMBAT, MOLOCH ON APPROACH AT 3 (O'CLOCK)"

Note: A rule my crew has established is that only the CO can call to General Quarters. This doesn't mean you can't pre-stage. Your crew might even make a habit of preparing by getting necessary gear and standing by where they need to before the call is passed. Once GQ is called they'll know to kick it to flank speed.

Another useful method, mostly for larger crews, is to separate comms by different nets.
Things like
ALLNET: All Net, for everyone, usually used general chitchat or for big announcements like GQ or Damage Control
COMNET: Command Net, for command positions like CHENG and CO to communicate.
AWYNET: Away Net, for the away team to talk amongst themselves without muddying main comms.
ENGNET: Engineering Net, for all of Engineering to talk to each other.

Again, if you've got 4-6 people you won't really need to separate comms. Large crews however, could benefit by reducing traffic on the lines.

Now, for a list of random useful terms my crew has used and some terms I think might be useful.

• COMMANDING OFFICER: CO, the Captain.
  
• EXECUTIVE OFFICER: XO, the Captain when the CO is not available.
  
• DEPARTMENT: DEPT, A collection of personnel who fulfill certain roles and have certain responsibilities.
  
• COMMAND & SECURITY: C&S, Command, Navigation, Security.
  
• MEDICAL: MED, Medical Care and Materials, Gardening, Research.
  
• ENGINEERING: ENG, Power, Maintenance, Repair.
  
• DEPTARTMENT HEAD: DH, Designated by the CO who takes control of a Department and it's crew and activities.
  
• SECURITY OFFICER: SECO, Maintains sub and crew stability and safety.
  
• MEDICAL OFFICER: MEDO, Maintains crew health and wellbeing, sub-board garden, medical supplies and materisl, research.
  
• CHIEF ENGINEER: CHENG, Oversees all Engineers and Engineering activities. reports directly to CO.
  
• MECHANICAL OFFICER: MECHO, Operates, Maintains, Repairs, and Inventories all Mechanical equipment aboard and maintains the hull.
  
• ELECTRICAL OFFICER: ELECTRO, Operates, Maintains, Repairs, and Inventories all Electrical/Electronic equipment aboard.
  
• ASSISTANT: AST, Assists Departments and other personnel, self-assigned, assigned by CO, requested by DEPT.
  
• GENERAL QUARTERS: GQ, Call to battlestations. Crew prepares the sub for Combat and Damage Control activities.
  
• LIBERTY CALL: Time to go AFK, complete random duties, fulfill supply orders, etc. Free time.
  
• AWAY TEAM: The team that leaves the sub for any reason, exploring, mining, repairing the sub, etc.
  
• DAMAGE CONTROL: DC, Procedure(s) to save the submarine through repairing damage.
  
• BOW: The front end of the submarine.
  
• STERN: The rear end of the submarine.
  
• CONN: The control center.
  
• LIBERTY: Free time.
  
• WATCH: A post someone stands, Reactor Watch, Supply Watch, etc.
  
• MATERIALS & EQUIPMENT: M&E, Tools, Parts, Materials, any kind of supplies you can think of, all of it falls under M&E.
  
• SUPPLY OFFICER: SUPPO, Designated crewman who manages the main supply system, buys/sells.
  
• ASSISTANT SUPPLY OFFICER: ASUPPO, Assists SUPPO.
  
• CRAFTING OFFICER: CRAFTO, Designated crewman who manages the main crafting system, crafts/deconstructs.
  
• ASSISTANT CRAFTING OFFICER: ACRAFTO, Assists CRAFTO
  
• LOW OXYGEN CONDITION: LO2, sets Low Oxygen Condition procedures.
  
• ALL HANDS:, All Hands, the entire crew.
  
• OCEAN BREACH: OB, major hull breach exposing the sub interior to the ocean. Diving gear required to fix due to extreme pressure.
  
• UNDERWAY: Out at sea, doing a mission, roving the depths.

Establishing consistent, step-by-step procedures is excellent in improving efficiency and increasing crew survivability. Having standard processes for certain situations.

The biggest example that likely everyone has ever heard of is:

GENERAL QUARTERS (aka Battle Stations)
Bring the entire ship to combat readiness, everyone has a battle station.
The basic process my crew uses is:
ALL HANDS don diving gear or breathing masks. (Depends on space and role.)
ALL HANDS return to their battle station.
Ex of battle stations:

• Captain to Navigation
  
• Security to weapons/armory
  
• Medical to sickbay
  
• Electrical Engineers disperse to Reactor, Electrical center, Navigation (Depends on crew complement.)
  
• Mechanical Engineers disperse to Engineering, Fabricator, about the ship to repair hull breaches. (Depends on crew complement.)
  
• Assistants disperse to aid in Damage Control efforts.

One of the most important procedures to have aboard, increase sub and crew survivability exponentially. Especially when fighting something like a Moloch or Thalamus or Pirates.

Coilguns and railguns are your best friends in the cold Europan sea, and running them well is key to your survival. This is the fast guide to keeping you and your shipmates in the belly of the Dugong rather than the mudraptor.

• Don't hold down the trigger. I know it's tempting, and it will increase your chances of landing a hit, but except in the direst of emergencies, you will be better served making every slug count than emptying your limited ordnance bays in a blind panic and then getting eaten by the mudraptor that wiggled through the hull while you were fetching another box of ammo. An ounce of sniper is worth a pound of suppressing fire.
  
• Keep an eye on the green bar at the bottom representing your supercapacitor charge level. Learning to ride the recharge will take you much further than blind clickmashing, and prevent running out of juice in a critical moment (as well as mysterious bouts of "why does it just go click?" if your capacitors broke while you weren't looking)
  
• Regular ammo does the job 98% of the time. Aim with care, land most or all of your hits, and you won't need to get fancy unless you've brought a coilgun to a nuclear railgun fight, or you're engaging a pirate sub. In this eventuality, don't try to save money by bringing ammunition home with you.
  
• Don't get cocky. You will not always have warning before the alien horrors are clawing at the hull. You will always have warning before they're inside the hull. Be prepared to run for the periscopes at any moment at the sound of a hull damage alert. Additionally, never take your eyes off the enemy you can see to go looking for the enemy you can't.
  
• Sometimes gunnery is deft operation of the powerful weapons mounted to your submarine. Sometimes gunnery is putting on your suit and going out on the porch with a shotgun. If you have an itch you can't scratch, don't wait around for the enemy to wander into the eye of your guns. You're going to have to resort to small arms anyways; may as well do it before you have a hull breach to deal with as well.
  
• Cover your divers. You have bigger guns and more armor; use it to keep your crunchies from getting crunched. Just remember to check your fire. The last thing you need when you're swimming for your life from a hungry crawler swarm is a coilgun hole in your suit.