When I am sailing and from time to time running my engine to at least leave the dock or come in I have everything on. When I am at
anchor or dockside I turn the engine battery off so it is available when I need the power and it is not drained. Your battery charging system should be wired to charge even if the switch is on or off. The negative switch will take it out of the loop as the negative is gone and it is not a battery anymore.