On ours, same setup as yours, I blocked/sealed off the duct work in the kitchen area, due to we travel with a Parrot, and he likes to be warm. Now the rear AC unit just does the bath/bedroom(Also blocked 2/3's of bathroom vent off to direct more air to bedroom, bathroom is small compared to the bedroom), and the front AC does the living area. Most the time, I set the AC in the bedroom, and the front is set to heat pump(Mine works this way?) or just a small floor heater to keep the front around 75 deg. or so.
On ours, the ceiling duct work runs the entire length of the Coach, common ducts for both units. I just separated them by blocking off the output side duct in the kitchen, first vent in the living area from the bathroom. Has worked well now for years for us.
2000 Newmar MADP 4060, 350ISC, Spartan MM, IFS 2011 Jeep JK, M&G Braking, 2014 MTI 27' Hog Hauler, Wireless brake control, 2006Ultra & 1989 Springer