They typically will fly off if they can find a path out of the ship. The idea is simple enough. Have the fighters with bobby AIs all docked in their happy little spaces. Use the structure tab, while in the ship they are docked to, to first enable all AI in the Fixed Docking Collective. Open all doors on the ship (unless your fighter bay is doorless) and then undock them all or one by one in the structure tab. They should fly themselves out and engage hostiles. Getting them to redock after the sortie is the only real problem you'll have. At the moment the AI tends to just chase things, kill them, and then hang there in space waiting for new targets. They do not Return to Carrier yet.