I had the same problem that you are trying to avoid. I had a 75 Merc. and 5 Merc. kicker. I installed an alternator in the 5 kicker to charge the battery while trolling; it was an accessory of the kicker and was sufficient to keep the battery up. Also installed a volt meter that gave me the state of charge of the battery, the volt meter was one that reads from about 8 to 16 volts from West Marine. My present setup is 15 hp 4 stroke electric kicker and it keeps the batteries charged.
