Whenever you are in USE Ac power from the generator or shore power is provided to the converter. In the converter the AC is CONVERTED into DC and provides DC power to the coach DC circuits as well as providing current to the house batteries and chassis battery for charging. So your batteries will not charge if the switch is not in USE. Here is a general guideline:
Boondock Camping -- not hooked to shore power -- switch in USE to provide battery DC power to the coach circuits. Also allows batteries to be recharged when the generator is run. Needs to be in USE to provide starting DC current to generator.
Generator operation -- switch in USE. Needs to be in Use to provide starting current to start generator. Needs to stay in USE to recharge batteries and provide DC current to coach circuits.
Driving down road -- switch in USE so that charging current from engine driven alternator will recharge house batteries through the BIRD/Trumbetta circuitry.
Stored -- in STORE. This electronically disconnects the house batteries so they don't discharge. If you store and have shore power connected, then the switch should be in USE.
I compiled a Owners' Manual for Axis/Vegas that augments the Thor general manual. My manual provides lots of information on how the systems operate. It especially focuses on electrical issues. Don't know what model Thor you have; however, there should be info in my manual that will help you. Here is the link:
https://1drv.ms/w/s!AiYx6DLSeiiP6UNyy_VYGDO0BW6L