You have two separate 12v battery systems in the RV. One (or more) are your CHASSIS batteries and they start the engine and power the driving functions. The second set of batteries are the HOUSE batteries, they power all the living functions of the RV. The two battery systems don't link together except with the "Boost" button on the dashboard. This button ties the two systems together while you hold it down to start the engine when necessary.
Often near the entrance will be one or more switches to isolate the batteries. When the RV is stored or parked, not in use, the switch is set to Off or "Storage." When you are using the RV or have access to 120v 'shore' power, the batteries can be connected. On some RVs a switch also near the door is known as the 'salesman's switch' which usually turns on some of the ceiling lights for showing the coach to customers. If you have a switch like that, the switch provides the 12v, but the switches on the light fixtures also needs to be turned on.
Another time both sets of batteries likely are linked together is when a 'charging' voltage of over ~13.5v is present. The batteries connect so they all can be charged by the converter/charger, powered by the shore cord or generator. They also connect together when the alternator on the engine is providing power driving down the road.
You need to take voltage readings of all batteries, then connect to shore power and take readings again to see if all batteries are actually being charged by your converter/charger. Fully charged batteries should be about 12.7v, charging voltage should be 13.4 or more, according to how depleted the batteries are.
You can read about your RV by going to the Winnebago website
and you'll find owner's manual, plumbing, and electrical drawings for your specific RV.