how many batteries do you have? one for the main motor, and one for the trolling motor, I have the on board charger also
just to charge my trolling motor, they main battery stays charged.
does your battery actually go dead out fishing? your alternater
should keep it charged.. I troll mostly with my electric which is really nice,,
that battery can last most of the day,, the battery for the main motor
never had a problem trolling for hours
anyway I just plug mine in when I need to.. it is a 2 bank,, like I said I do not have the main motor battery hooked up to it.. if it matters
I run a 70 outboard... sounds like an alternator to me... that is not charging the battery, I would take the alternator and get it tested, or do it your self with a meter..