I could be wrong but I think if you do this you need to use the battery at the end of the line (the one that has the trolling motor ground wire connected to it) as your cranking/acc battery. Other than that just be careful. I doubt you'll come close to draining your batteries with a 36v on that boat though. I battled strong wind with my 24v Ultrex for 8 hours the other day and it didn't seem to stress a pair of group 24 batteries much at all. If you do 3 group 29 Everstarts back there you'll be good to go.