This really isn't your answer, but I think I remember Chariot's method for charging both banks of bats. drawing a diagram might be easier...Someone mentioned isolation...
Our camper has a Powerline Isolater 33-53 made by Power Systems, Ft. Worth. It tells the alternator how many total amps the bats need and splits amps out to the chassis bats bank and/or the house bats bank. It will not let power travel backwards from the bat banks to the alternator or tie ea. battery bank. When no alternator power is available, the invertor (powered from the generator, shore power or house bats) supplies power to a 12v charger which keeps the chassis bats charged. The invertor charges the house bats when 120v is present. Since the generator uses the chassis bats to start, theoretically you would always have a way to charge bats and wouldn't need to tie em together. I don't know what it would do to the Isolator, but you could tie the wire feeding the two bat banks together as the lugs on the Isolator are only inches apart. Understand, when your bats are tied in series to make a bank and you have different bat capacity out of ea. bank, you will have issues of one bank drawing off the other.
Vans in Indy IN. replaces the voltage reg. to some type of smart circuit in the alternator.
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