In that case I would not do anything different. When you put the isolation in use a continuous rated solinoid (sp?) Put a switch on the dash that is connected to the ignition switch. It will leave the batteries connected in the on position (if the ignition is on)but in the off position they will...
With all chargers charging at one time. The only problem I see is that you may have to high of a voltage (IF) you have a deep cycle battery as your house battery. But as long as your charger on your generators AC output is a smart charger and it is not in equalizing mode it will quickly drop...