I have the same model/year, but with a third battery - so in my case: a start battery for each motor, and one for the house.
Whether or not you're charging both depends on your motor and wiring. The Yamaha's have an auxiliary charge cable that should be connected to the "other" battery. If you have one battery designated for house, most likely that motor's auxiliary charge cable is charging that. It's a much smaller cable (14ga?) coming off of the motor's bundle, and would be connected to the post on your switch that is also connected to that battery - most likely "B".
If you don't have that charge lead, then I don't know how you could be charging both batteries unless the switch was set to "Both".