I do not know about 6 volt batterys in series....but If you had two 12 volt batterys in paralell and a two bank charger with a separate bank going to each deep cycle battery, you would not want to charge over 15 amps per bank. Charging any harder than that deep charging often is going to shorten the life of those batterys. A 50 or 60 amp resetable circuit breaker is required near the battery for the positive lead going to your trolling motor.