Sam,
I assume your batteries are connected to the alternators through the 1-ALL-2-OFF switch and the start cables. In this case, it's normal to run in ALL to charge both battery banks. However, you must then remember to switch back to the house bank when you stop. If you leave your banks paralleled in the slip on the shore charger, you tie them together as one battery and you're not helping your battery health.
If you rewire appropriately and install an echo charger or Blue Seas Automatic Charge Relay (ACR) you can leave the switch in the start position, charging both banks and pulling house power only from the house bank while at anchor unless ALL is selected. It takes some re-cabling, but it's a failsafe and foolproof way to prevent unintentionally leaving your banks paralleled or isolated.
I recabled my Californian last spring and have absolutely no regrets. I never have to touch my battery switches for normal operations, but they're there (outside the engine room) if I ever need to isolate or combine the batteries.