[quote=Heat]
Like the top fighter pilot on the ship? I was going more with many of crew being able to pilot the fighters.
[/quote]
I'd be inclined to think a complement of fighters would have their own pilots assigned to them; I mean, that's how it works in a real military and you need individuals who are specially trained for certain tasks. 
& by "flight commander" I mean the pilot who acts as commanding officer to the others. A flight is technically comprised of around 4 or less craft, and that's really all there is stationed on the ship.