A properly configured dual battery system allows electrical draw off of just one battery, leaving the other battery for emergency or auxiliary use. It is recommended to leave the battery selector switch on battery 1 or 2 but never on both. This way if you drain the battery completely down from using 12 volt systems, you always have the other battery to switch to for restarting the engine.
The position of the battery selector switch only designates which battery is being used and does not effect the charging of the batteries. Even if you select battery 1 or 2, both batteries will always charge when plugged into dock side power or when the engine is running.
When the boat is not in use and is not plugged into dock side power, it is recommended to place the battery selector switch to the Off position. This will prevent battery drain in case a device is left on. Even when the selector switch is in the Off position, the main automatic bilge pump is usually wired to one battery so it will still operate.