Let me start by saying I have an '05 Bounder 36Z with the same two "main and aux" switches. Frankly, I don't know why Fleetwood chose to use that naming convention, I always thought they should be labeled "chassis" and "house" but I never got a call from Fleetwood to ask for my input
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When you push either switch, it operates a contactor (a big relay) that cuts the battery in or out of the circuit. In my experience, they should be exercised occasionally, I've had weird problems like you mention and simply operating the switches several times cleared the problem. On my rig, the contactors are located above the propane tank inside a black box.
I don't have power seats or the RV level meter you mention so I can't address that.
I installed my inverter myself and connected them only to the house (aux) batteries, I can only assume that is the way all inverters are installed but I'm not an expert. Perhaps, someone else can speak to this.
As far as I know, the generator charges the house (aux) and chassis (main) batteries simultaneously, but again, I'm not the expert.
When you push the Aux Start switch, it cuts in the house (aux) batteries so you can start your rig if the chassis (main) battery is dead.
Hope this helps.