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My charger goes to each battery. The way Cobalts are originally wired, the Blue Sea ACR ends up combining the batteries. The way to avoid this is to move the ACR leads to the load side of the switch so the only time it is allowed to combine is with the battery switch in the on position. The drawing below shows how you should wire it so that the battery charger that has 2 bank outputs doesn't cause the batteries to combine.

If your charger only has one output, you can leave the ACR where it is and the ACR will combine and charge both batteries although not ideal in case you have a battery that is failing.