You don't need the isolator unless you're playing the system with the vehicle off often. Also, I read your sig (which I hadn't before) and you mention you're mixing wet and AGM batteries. Wet cells hold a lower surface charge than AGMs so when you mix them, the wet cell will rob the surface charge from the AGM.
To compound that problem, the big three grounds plus the factory grounds are causing the majority of charge current to hit the front battery, leaving the rear battery undercharged.
The only ground that should be connected to the front battery is the factory ground. From there, you should run a positive and negative run to the rear battery and then, the rear battery should be grounded to a shock tower... two grounds would be even better, with one to a shock tower and the other to a body panel. Big three grounds should go from the alternator case (or engine block) to a shock tower and a frame member only.
Current follows the path of least resistance, so when your front battery is grounded better than your rear(s)... it will always get the lion's share of charging current.
