badasshybrid,

Something is missing from your description.

If you are running a dual-battery switch then everything runs off the Perko common and nothing goes directly to a battery except a float switch/bilge pump when applicable. No exceptions. Then the switch in "OFF" provides total isolation between the two banks for AC charging providing for independent battery profiles and programs.

If you're using an ACR/VSR then the scheme will definitely change according to the particular brand. And in most cases you'll have to add a supplemental switch for isolation during AC charging. A bass boat is a little different because the outboard motor has a very small alternator or stator comparatively, which cannot charge a depleted bank with a considerable amp/hour capacity. So the trolling motor bank remains in total isolation from the boat's electrical/charging system and is completely dependent on AC shore charging for restoration.

David
Earmark Marine