If the two house batteries are 6V batteries (typically golf cart batteries), they should be connected in series, the positive of one to the negative of the other, and the remaining terminals to the RV (- to ground, + to the positive system). If two twelve volt batteries, they should be in parallel—the two positives together (to the + system of the motorhome), and the two negatives together (to ground). In neither case should a battery have its positive terminal shorted directly to its negative terminal.
I think your chassis battery was dead or nearly so. On my '98 Coachmen class C motorhome, the generator starter is powered from the chassis battery, not the house battery, which was not what I expected initially. I don't have any slides, but they might also reasonably be connected to it. The chassis battery is often not charged by the converter.
If it was dead or discharged, it could be because of age (if it wasn't replaced with the house batteries) or because something was left on that should not have been—maybe mirror heaters or a cab area dome light, for instance.