Ok, I've gotten to the point where I can start working on this again. Here's what I've changed around.
1. I'm trying to see if a traditional shuttle bay will work well with this design by raising part of the back of the saucer. I haven't done anything with textures yet, which is why they look stretched in the pictures. If I go with this design, I'll definitely fix this.
2. I've moved the torpedo launcher in between the phaser banks and the light emitter thingy on the bottom of the saucer. I think it looks good here and it doesn't cover up the phasers so you can still use them, but if I keep this here, I'll have to redo the light maps and the textures to make it cast a shadow, which may not look very good. I'll have to play around with it and see.