Just went through this myself.
What ACR setup are you using? It might help for me to give you better pointers.
1 - The ground from the isolator needs to be solidly grounded at a point that both batteries ground to. (As it switches topping each battery one at a time, picture it needing a complete circuit to each battery one at a time.) Sounds confusing, but each battery should be grounded to the block independently, and the rear ground bus is attached to the block as well, or directly to one of you batteries. In essence creating a big web of grounds that has everything interconnected. I only point this out because
as long as all your grounds are already done properly, (no corroded wires) you should be able to ground anywhere and have it work. I had one bad battery ground cable that was throwing the system off that needed to be replaced. I myself ran a wire directly form the ACR to the rear ground bus.
2 - The alternator usually feeds directly to the starter. On mine its a 10 gauge orange cable.
3 - It sounds like you have the Blue Sea setup with SI (starter interrupt). The wire to the SI port on the ACR is
optional and only needed if you want the batteries completely isolated when your are cranking. Example: You have a fancy radar setup that shuts off abruptly when you crank the motor. I contacted Blue Sea about this and they told me that you don't need it unless you have very sensitive electronics on one of your batts. (Notice that its an 'optional' dotted line in the instructions.) I left it out. If you want to use it, it has to be wiring into a lead that is only hot
when you are cranking, NOT just a switched lead. If you hook it up to a switched lead, like what your stereo is on, the ACR would never link the batteries for charging when the engine was running which would defeat the purpose of having it.
Let me know if you need more help!
2nd Battery/Isolator Relay Switch
