Originally Posted by pjespers
Here's my setup. My 2000w inverter/charger is connected to the house batteries. Some folks use a switch rather than an isolator.
With the set-up in this drawing, you are only half protected. The isolator (back-to-back one-way valves) is preventing the house battery from powering the starter. But the starter battery is not protected. If the house battery discharges below the starter battery by the turn-on voltage of the isolator (less than a volt), the power from the starter battery will take the same route through the isolator as power from the alternator would. The starter battery would discharge into the house battery until its voltage less the isolator loss becomes equal to the house battery. It is possible to run both banks down to the point where the bus will not start.
I'm not sure what you mean by the alternator not having enough power with the correct isolator wiring. If the alternator has an internal regulator, and you cannot wire a voltage sense wire to the starter side of the isolator to compensate, it is possible that the slight voltage loss through the isolator is enough to prevent the batteries to charge to 100%.
The other possibility is part of normal isolator operation. If the batteries are grossly unequal, the weaker battery gets ALL the alternator output until the voltages equalize, either charging up the weak one or discharging the strong one until reaching the same voltage. If you have run down the house battery when camping, driving home and observing the bus running off of the starter battery without alternator assist while the house battery recharges could be scary if you don't know what is happening.
It would usually be better to use a battery join switch than only half an isolator. The set-up in the drawing may work for you, with good batteries and conservative power usage, but copying it may get someone else stranded in the boonies.