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.