Relax, when you launch a wing he will use both fighterbays.. Fighterpaths are named Bay01 to Bay04 and it's parent is Detail1.
I did it for the Orion MK2 with a total of 2 fighterbays and 8 paths. If you're launching something big, the game uses both fighterbays so the ships wouldn't collide.
Immagine my surprise when I saw only two Athenas come out of the bay! I went "WTF?.. What' did I do wrong this time" only to fly around next time and see the other two coming out of the other bay....
ERm.. I think it's 8000 polys total for LOD1 with turrets. The main ones are 116 polys each, others are about 12, so the ship hull itself is about 4000 polys...