Electrical puzzle

I've got an issue with our new 28'Argosy that I'm trying to figure out without digging into all the electrical stuff (That will come later, but I have more pressing concerns). It has three batteries- a chassis battery and two deep cycle house batteries. The engine and first battery are next to the driver in the correct spot but the second house battery is under and behind the univolt in the storage. I thought it was a funny way to set it up, but I determined that it was separately wired to part of the DC panel. So some of the system is one battery and the rest is the other. Now I just found out it is not connected to the univolt. Some of the lights started to dim after a couple of hours so I plugged into shore power- half the lights stayed dim. Then I pulled the plug and started the engine. The dimmed lights immediately became brighter. So that means (to me) that part of the DC system is charged by the alternator, and it appears there is no isolator. Is that just wrong, or is there a wisdom I'm not seeing? Other than that, the PO kept it up very well.