I have duals in my 84, both are on the flatbed.  The main is on the passenger side so its a shorter run to the main truck supply and starter.  (I have a 350 in that truck)  The secondary is on the driverside of the bed and up until the isolator died the main pos cable went straight from the alternator to the isolator.  The isolator split off and ran the main first then when it would basically trickle the main and charge the secondary when needed.  It worked awsome till the damned isolator died, then I just ran the battery +'s together and it still works great but I need tp put my relay in like brainless   I have never had a problem with using different batteries together in any dualed rig.  The main is a group 24 and the secondary is a 31c which basically amounts to a semi battery.