Do yourself a favor and check out the Hellroaring isolators. Pete (Cyclone) did a 'why' and 'how-to' here:
http://www.epicmarine.com/how_to.htm The thing that makes sense to me is that the cheapest isolators will allow two banks to discharge separately, but charge both banks as one - the result is somewhat overcharging one and somewhat undercharging the other (both bad).
The more expensive isolators handle both sides independently in both discharge and charge cycles. The problem with most of these is that they always drop the charging voltage by 0.7 vdc by nature of their internal diodes. Unfortunately, this means that both banks are always undercharged by 0.7 vdc.
The Hellroaring ioslator handles both banks completely separately, and the voltage drop is much less than the diode versions. Pete mentions that the this isolator's probably overkill, but the reasoning behind it is sound. And friggin batteries are expensive, huh?