First off, know your ship ahead of time. Know where your hull and balloon engines are. Hulls are most likely to be in the center of the ship and control the ship. WIthout it, your ship doesn't move. The balloon engines control the ascension and descension of the aircraft and serious damage causes a rapid decline in altitude. The engines in the back of the ship or whereever they're located control turns.

Focus your primary objective on the hull because if the balloon can't move, you're basically a sitting duck. Second important object to repair is the balloon engine due to the maintainence of the balloon's altitude. If you don't repair it, might as well forget your chances of living. The engines are the third most important objects to repair as without proper maintenance could lead to the pilot not being able to turn and make evasive manuevers under enemy fire. Last thing to repair are the guns as the gunners can repair them. If you repair everything else, then by all means repair the guns.

The loadout I use and you necessarily don't have to copy my exact loadout is: buff hammer, repair hammer, chemical spray, and lookout lens.

Once you understand the importance of what to fix first, you can prioritize what to fix during the heat of battle.