Usually, the AI takes the first available (free) path for launching, and the nearest available (free) path for landing. Unfortunately, it sometimes picks also the first path for landing too, even if it is not the nearest one, or it suddenly launches from the path's 6-12 i.e. (that really sucks, I hope the SCP will add at least selectable fighterbay-subsystems for arriving/departure cues).
If you want the fighters to launch from a special hangar, make two subsystems, add the paths and they will usually start from path 1-6 (depends how many paths you edit to the fighterbay-subsystem). Controlling their landing is more difficult, if not impossible.