From what I understand, if you hook up two batteries in a parallel circuit( + from alt. to front, then to back battery) the front one will recieve all the charge, and the rear will get very little, unless you can isolate where the charge is going.
Part of the problem is that one of the batteries is in the back, using long cables to reach it. If it was underneath the hood, it would be a shorter distance to charge, since there would be almost no power loss in the short cable that would be needed there.