OK, You need to find out why the isolator solenoid is not being energized. Could be something simple like a fuse. Then the house batteries will charge from the alternator.
If the rig design is to not charge the chassis battery on shore power then you should correct that with say a Trik L Start or a 2A battery maintainer.
Something is wrong with having to replace batteries every 2 years. Kept charged it should be 5+ years. Consider buying a $50 Sears clampon DC ammeter and find out what is draining your batteries as it would have long ago paid for itself with increased battery life.
Why did you switch to 12V house batteries? 6V are better suited for house batteries, more power and greater number of recharge cycles. Otherwise 12V are OK.