I have an RV with dual batteries.  It uses a battery isolator to isolate the
circuits.  The alternator charges both batteries, but if the house battery goes
dead current cannot flow from the starrtng battery.
 
The problem with this is that if your starting battery goes dead, the house
battery doesn't help you start.  So you could do what they do on boats, have a
switch that allows you to start using both batteries, then when you camp you set
the switch to run the stero etc. off only the deep cycle.  Definetly the cool
setup, but you have to remember the switch.  Any book on marine electric systems
will have diagrams.  The switches are cheaper than isoators, too.
 
Bill w/ 67 split, in WI