yeah and dont worry about it's debris haveing weight, because if the Prometheus is destroyed, its game over. They have anti-gravity too in case you meant a literal way to have it up. They have artificial gravity on the ship, so if they can make gravity without centrifugal force, they probably can take it away. Besides there arent any regular engines on the bottom of Prometheus.
The way I think we should do secondaries is to make them 2 or 4 depending on the fighter and make em really friggin powerful. Only the X-302 has em. The Prometheus has probably somewhere around 8 missile bays, 4 on each end. Or possibly mounted on the wing-ish things on turrets. Because we know it can fire directly behind itself. Remember that 2 X-302 missiles took out an Anubis supership's reactor/shields/whatever so they have to be pretty damn powerful.
We shouldnt have any support ships, IMHO. We're making Stargate, not Freespace with Stargate ships. The only support ships are the carriers/cruisers' fighterbays. But I guess support ships are possible. Just remember, they'd have to physically put the missiles back on the wings. SPeaking of which, how are we going to get the missiles OFF the wings in the first place?