Here is what I do
I don't have an automated charging system, so it's up to me to make sure my batteries get charged. I have two house banks connected to the 1B2off switch, and a starting battery. I start the engine using the house bank that I will be using (or have been), so that it will receive the charge from the ho alternator, and 3 stage regulator. There are two switches that connect either the starting battery, the house battery, or both to the engine/alternator. This way I have a battery to start the engine when needed.If you only have the two batteries you should alternate use of each one, always saving the other to start if the current house battery will not.