Seeing as how this is your first post, let me be the first to welcome you to the IRV2 forum.
"Generally" the house batteries are charged by the vehicle alternator when driving. An item called a Charge Solenoid will kick in to tie the two battery systems together whenever the ingition key is on. The Aux Start switch should only be needed when the unit is not running and you need the house batteries to help jump start the chassis batteries to get your engine started.
However, not all RVs are alike so your system may be different. I'd suggest that you go to your profile and add some information in your "signature" section. Include your name, RV information, and towed vehicle info. That way whenever you post, people will see what you have and they'll be better able to answer your question.