I don't know much about the newer units but if the electrical system is anything like my 1984 310 then I can give you a general idea of how the ATS units are setup. Of course none of this will likely apply if you have a 50 amp service.
On our 310 one of the two ATS boxes is used to switch between shore power and generator power. If you're connected to shore power the ATS box routes power from the shore system to your main electrical circuit breaker panel. However if you happen to start your generator while still connected to shore power the ATS box waits for the generator to start producing the correct voltage (approximately 15 to 30 seconds) and then disconnects your coach from shore power and switches your electrical panel over to generator power. This effectively isolates the generator power from shore power. Trust me, you never want the two systems to be tied together at the same time
The generator our our 310 has to output feeds that provide roughly 25 to 30 amps each. One feed goes strictly to the second ATS that feeds the rear air conditioner and the other feed controls the rest of the coach.
When connected to shore power on our 310 you can only run one air conditioner which is controlled by a rotary switch in the kitchen area. However if we are on generator power we can set the rotary switch to front air conditioner which allows the front air conditioner to run. While on generator power the second ATS box switches the rear air conditioner feed line from the shore power circuit to the second power feed coming out of the generator. This allows us to run the second air conditioner.
This is a somewhat simplified version of how this works. Also as mentioned above this may not apply to your motorhome.
Now in answer to your low voltage question, my first guess would be you have a bad connection either at the plug end of the shore power cord or else in the box where the shore power cord connects in the coach. Check those connections closely and don't be surprised if you have to replace the male plug.