Add to your signature the model, year and horsepower of the boat and motor.
Has the battery setup always worked fine, is this something new or are you just now noticing it?
Have you checked for the correct connections via the battery switch and batteries?
Very rough drawing:
From what I remember it is suggested to shut the engine off before rotating the switch , so as not to possibly damage the charging system due to a sudden spike.
Using a battery charger periodically is needed in most cases.
Some charging systems have a low output rate and the motor may need to run for 24 hours to achieve a full charge to the battery.
It almost sounds like the two batteries are not connected together with the negetive terminals.