Second question first- NO. You shouldn't have to have the "Emergency" switch set to On. The other two should be on unless you have reason to turn either set off.
The Xantrex should charge house batteries anytime you are plugged in. Also, on the back of the battery compartment wall is a fat, black solenoid labeled Trombetta, which should be energized if the #19 Output LED on the Vansco module to the right is lit. That solenoid connects the chassis batteries to the house batteries any time charging voltage is present above a preset level. If you are charging the house above ~12.5V, #19 should be lit and the solenoid should be connecting both battery strings together. If #19 does not light with charge volts high enough, you may have trouble on that circuit of the Vansco. More likely, the solenoid has burned out contacts and doesn't keep the chassis string charged. You can get a new solenoid at Murcal.com, or switch to a Cole Hersee #24059 (ryderfleetproducts.com) if the Trombetta is not readily available. Get ready for some issues w/getting the old Trombetta off the back wall, as it is thru-bolted on the metal plate w/nuts on the back (probably nylocks to add insult to injury). I never did get those off but did get them loose, & after prying the old Trombetta off I drilled & self-tapped new crews just above the old ones for mounting the new Trombetta, and used the old screws as a "clip" under the new solenoid's bracket edge for easier uninstall/reinstall in the future. Many carry a spare solenoid for just this occasion.
BTW- Welcome to iRV2 and hope to see you at an ACA rally soon!!
Baja-tested '08 2-slide 36'
Alpine: The Ultimate DIY'er Project