No, you should not disconnect the boat battery when charging. Connecting to shore power does not automatically mean that your batteries are disconnected from the system. When plugged in at a dock or marina, the shore power charger will automatically connect to your boat's battery bank and start charging. You should not disconnect the boat batteries when plugged in because it could cause a short circuit that damages the batteries. The only time you should disconnect the house bank from the boat's electrical system is when there are problems with your charging system or if you need to work on something that could be damaged by electricity.