I've made a few changes to my top view of the design.
I'm basically trying to move away from the secondary hull being long ways from the saucer and instead running across.
The saucer actually connects in the centre of the secondary hull so the secondary hull rises halfway above and below the saucer.
The shuttle bay is central so it's actually level with the saucer.
Sublight engines are on the back of the secondary hull.
The nacelles are connected to the secondary hull centrally just slightly raised above the saucer but the nacelles are connected to the saucer by pylons.
These pylons also house the forward Torpedo launchers, two launchers per pylon. The aft launchers are located on each side of the shuttle bay.
Is my description adequate or is there any confusion?