RE:  Charging with a battery isolator
If you have the right isolator the isolator takes over the business of
regulating the voltage to both batteries, in fact the regulator in the
alternator is disconnected. This eliminates the problem of a voltage drop
and consequent low charging voltage on the aux battery.  see the following:
 http://www.geocities.com/harald_nancy/dualbattery.htm 

Also http://www.surepower.com/Applications/RV/batiso.asp

If you want to move everything internal (lights, radio, etc) to the aux
battery you will need to rewire the 12v source for fuse 3 in the fuseblock
so that that fuse is fed from the aux battery and not the starter battery.