Unless there is something wrong with your boat, it won't harm anything no matter what you do because the trickle charger is introducing less amps for sure (and similar volts) then what the alternator does. Sometimes I charge while switch is on to listen to the radio while charging (and maybe wiping down the boat), and sometimes I have the switch off. But in either event I do not disconnect the battery to the boat electrical system.
"All modern passenger vehicles come factory equipped with alternators. Peak amperage ratings range from 100 to as high as 275 amps."