We have the same setup you describe. Only difference is the original stock alternator charges the cranking battery and a high output for the house bank of 4 Trojan 6-volts. I first bought a Link 20 for 2 banks then realized the craziness. Returned it and went with a Link 10. The simple volt meter for the cranking battery is sufficient. Like others I left the 1-2-Both switch in but the 4 house banks are always set as a single bank. Only reason to keep the switch is to isolate if you lose a cell as Dan y says. One thing I did add was a "jumper cable" switch between the house bank and the cranking battery. If the need ever arises I can close it and start the engine off the house bank. Another use for the switch is if the high output alternator fails the OEM alternator can stand in to charge the house bank. That actually happened once. All the batteries are flooded cell lead-acid.