Re: on board chargers or portable
On board chargers are plugged into AC power at the dock, in your garage or storage building. They aren't even connected to your engine so no -- it will not affect the engine charging system. They do nothing unless plugged into AC power. If you are trying to charge the batteries on the water, then you need a dual battery switch, an isolator, or ACR and even then, your engine alternator will not likely keep up with the demand unless you run wide open for hours and the engine has a fairly large alternator. There is no free lunch in the "charging" system for a boat. What you use must be replaced. How that's done is with the engine alternator or an on-board charger that works like a portable, only is permanently installed in the boat.
