Bruce,
It sounds like you have the apples mixed up with the oranges.
I will be doing a seminar on this in Spearfish, but the short version is your bus batteries are not getting charged while your engine is off regardless of how long you run a generator or if you are connected to shore power unless you have a battery charger dedicated to the chassis batteries, and it is turned on.
The house batteries are charged automatically when the engine is running, when connected to shore power and when the generator is running because your inverters are on all the time and when the engine is running the alternator is charging them.