First, I would check the generator output. There are probably two circuit breakers on the generator, be sure they are set correctly. And, yes, you use your digital thermostat to control the AC's. Check your thermostat to see if the HVAC system is working by just turning the fan to the ON position. If the fan doesn't run or if the AC's still don't come on, then you need to plug the coach in and see if the AC's turn on with shore power. Finally, the transfer switch should be checked.
On the auto generator start, I am not sure when this was added as a feature for Monaco coaches. Basically, the system monitors the batteries, and if the battery charge get too low, the system automatically starts the generator to charge the batteries. Neat feature, but scary the first couple of times it happens to you, you'll wonder if your generator is possessed.
Wayne Lee
Out West Somewhere
2016 Forest River Sunseeker 3050DS Class C | Hummer H3 dinghy