Its amazing to me that this is always a question. The Yamahas have an Aux Charging circiut feature for charging two batteries separately at the same time. All that is required is a cable. Yet it seems the dealers never install or suggest it. The idea that you would have to remember to switch batteries to charge them is just stupid. And you should not run on both because if you have problems, BOTH will be run down and you will be stranded. An ACR (with SI) is another way if you don't have the cable.
The other thing to note is that Grady wires the House circiut to be powered by whichever battery that is connected to the motor. This is because they don't have an ACR or an Aux charging cable so its the only way to always have House power. When you have an Aux cable or ACR, you can separate the function of the batteries to make make one a STARTER battery and one a House battery. You do this by moving the house feed from the "Feed" of the battery switch to the positive terminal of the HOUSE battery. This makes your house run on a different battery than your Starter circuit. You don't have to remember switching anything. You won't be cycling down your starter battery by running the house with the motor off. The switch will still enable you to use either battery or both for starting.