No, secondary maps have to be in the "maps" folder, where all model textures should go. The missile pof's should be in models. That's not saying it's what is causing your problem, but it's certainly possible. The rest was explaining why, so feel free to ignore it.
The missile spawning fighter thing is possible, if by fighter you mean additional missiles with a small fighter pof attached as the missile and the "bomb" flag set to be able to take it down. Or you could use a swarm missile launch that just spits out x number of missiles.
Actually, nix that. If you do set everything with the bomb flag, I'm pretty sure that missiles will not be fired at fighters. That may have been changed, but I'm just not sure.