So when I started moving things to upgrade my wiring I see:

Alternator -> Car Fuse/Distribution Block -> Car Battery

would the proper setup be:

Alternator -> Personal 2 way distribution block -> Battery Isolator -> Battery A -> Car Fuse/ Distribution Block
-> Battery Isolator -> Battery B


or

From battery isolator to batteries

Alternator -> Personal 2 way distribution block -1-> Car Fuse/ Distribution Block
-2-> Battery Isolator -> Battery A
-> Battery B

 

The isolator is automatic. It focuses on charging the main battery and charges the secondary battery when the main hits a certain level. If the main dips, it switches back so the main is constanly within a certain range.

The main goal is that I have the alternator charging both batteries and have the batteries isolated.... one is for the interior inverter/car audio/etc and the other is the main vehicle battery.