as far as the charging system on the motor, no it wouldn't hurt it at all. as a previous post said, the cranking battery will not last IF hooked directly to the trolling motor batterys with out some sort of isolater. deep cycle batterys can handle the discharge, cranking batterys can't. if you really want to charge off the motors alt. I would recomend using a stay-n-charge system. it isolates the cranking battery from the discharge of the trolling batterys, and only connects when the alternater is charging.