In the top right of the port you will come accross the Eutopia Barracks. The Eutopia Barracks allows you to purchase additional crew members to properly staff the ship. It is recommended to have as many crew members as a ship can hold. They can be purchased by clicking the the green icon. In addition to buying additional crew members you can sleep for 6 hours to progress through the night instead of braving the seas in darkness.
Once you can no longer afford new crew members the icon will be grayed out.
Travel past the gate and head to the bottom edge of the port to speak with a soldier on guard duty. He will provide you with a special gun for your ship.
In the top left of the port you will come across the Construction Yard which allows you to choose your ship and gun configuration.
Within the Construction Yard you will see the above interface where you can drag "chips" into place to configure your custom ship. On the left you can drag whichever ship you prefer to use into place. Ships have varying health, armor, gun placements, and max personnel. On the right you will see your guns as red "chips." Drag the red ships into place to configure your gun placement.
On the right side of the port you will see Al's Store. Here you can purchase a variety of ships, guns, and perks with the right amount of dubloons of course.
Within the store you can drag the various "chips" into the slow in the lower middle to examine what is provides as well as the price.
Talk to the robot on the dock for an extra boost of dubloons, and once you are ready click set sail and begin your fight to unit Eutopia.