If you must disconnect the battery I recommend the disconnect on the positive side.
This will allow you the get 12v from the battery (behind the disconnect) and still have a working ground for the breakaway circuit to use on the chassis.
If you choose to disconnect the negative side, you must run the ground for the Operating unit and the reed switch/Noti light back to the negative terminal of the battery.
Either way will work.
The coach will illuminate the brake lights on the Denali if you have run the tow wiring to those rear taillights and connected everything properly.
Let me know here, or on a PM if you have further questions on that AFO system.