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This greatly varies on what was installed in the boat. How many total lines are coming from your charger?
Ok, another way to tell is look at the engine battery. There will be the large wires for the engine, small red and black for the boat, and if there is a thrid set of red and black, that is the battery charger. That would mean that when you plug in the charger, it would do the trolling motor battery and the engine battery as well.
The engine has a stator on it that produces voltage when the engine is running to also charge the battery, but only the one for the engine.
Does this make sense?