You guys are driving me crazy talking about this stuff so I have to answer
even though I have done so in the past: 

1. Do not use a dual battery isolator (robs too much voltage from a VW
alternator); use electrically operated relays instead. 

2. You can fit a deep cycle marine battery behind/underneath the driver (of a
Vanagon) if you allow the battery to stick up slightly higher than normal and
then fabricate a rug/tin covering to hide it. If you have swivel seats then
trim away the right rear corner of the swivel base so you can still swivel you
r seat without hitting the battery. 

3. Do not ever wire your batteries together since the one will drain the
other; always use relays to keep at least one of them disconnected when the
motor is off.

--Derek Drew

<---- End Included Message ---->
Derek,

Correct me if I am wrong,... I often am. 

 The Ideal situation would be to have a dual output alternator (one with two 
windings) connecting to seperate circuits: one would be the regular van 
battery. the other would be wired to three golf cart batteries (instead of the 
deep cycle battery).  I think the would be wired parallel, but I am not sure.

This configuration gives a complete separation of the two battery systems.  
The problem with the deep cycle batteries is that they are designed to drained 
completely and then recharged completely, the golf cart battery arrangement is 
ideal for shorter, medium to light usage and then topped off with a recharge.
The problem would be coming up with a dual output alternator for a VW.  

** As an aside: in putting together my latest fire truck project I used a 120 
amp dual output alternator one side connected to the truck battery, and the 
other side connected to (2) 8d auxillary batteries.  The truck batteries are 
continually topped off with a shore power connection.  I used the deep cycle 
because those emergency lights suck the power like nothing else.