Dual Batteries And Charging

I'm in the process of cleaning up the wiring on my new-to-me old jeep. In addition I'm putting in two batteries and running almost all my accessories through a heavy-duty, separated in key-off auxiliary circuit. I've set up several similar systems before with good results, I've have a good understanding of 12v electronics, so I know there's lots of ways to do this. I could go on and on but I made a couple quick diagrams to simplify input. For now, lets assume that I've fused everything properly and used the right size wires/cables for the application. I'm really searching for opinions/ideas on the positioning of components for the safest and proper battery charging.

My Components:
-starting battery
-auxiliary battery
-140 amp 10si alternator
-battery separator/isolator
-250 amp bussbar / power junction

Goals:
-separate the two batteries in the key-off position
-Run most or all my electronics and accessories off the auxiliary battery through the new aux circuit
-optimize the potential of the entire system

Questions:
1. As seen in the diagrams, the main difference between them is the location of the separator/isolator in relation to the batteries. I'm thinking about this in terms of the direction of charge current coming from the alternator. Which would provide a better charging system and why?
A. Connect the batteries at the main junction as in diagram 1? (Charge current flows to both batteries depending on demand)
B. Connect the batteries directly with the isolator between them as in diagram 2? (Charge current flows through the auxiliary battery into the starting battery)
C. It does not really matter, both schemes will work just as well
D. I've got it all wrong and there's a better way

2. I feel like Ive got everything fused properly so fuses are not shown below...but...what do people think about fusing the alternator charge wire? Seems like there's lots of opinions out there. For now I'm running a 140 amp 10si with a 4awg cable for the charge wire,..and it's fused with a 125 amp breaker.


Diagram 1:



Diagram 2:

 

The charge wire generally goes to the isolator and a wire goes from the isolator to each battery. Most isolators have 3 terminals but they all come with a wiring schematic.

 

Daryl, thanks for the quick reply. I'm using a 200amp continuous duty solenoid to separate the batteries. So I guess its not technically an isolator. I've run these with good success in dual battery systems, but always as a way to simply add a battery to an existing system. Right now I'm kind of redoing everything, including the upgraded alternator.

 

I used a Perko Switch and wired it like diagram #1 on the link here:
http://www.perko.com/images/catalog/pdf/Fig 8501-8504 Inst (8500INS1).pdf

 

I'd go with the perko or cole-hersey switch. we use them on firetrucks and boats. they work great.

 

Current/voltage flow is the same both diagrams. Depending on where the isolator/relay is located distance wise between the batteries, may have a slight resistance change if the wires are the same gauge.

 

Hey Walt thanks for that simple input. I've probably been overthinking this but its always nice to bounce ideas off folks. I've gone with the first schematic mainly due the way I wanted to route the cables. And I've already got the 200 amp Cole-hersey continuous duty relay.