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I have a 12-24 volt trolling motor along with a 12 volt cranking battery for my outboard what would be the best way of hooking the batteries for my trolling motor to run on 24 volt and what would be the best sytem for charging all 3 batteries
 
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When I bought my boat, it had 3 batteries - 2 for the 24v trolling motor and 1 cranking battery. After fighting it for one summer and continually getting a dead cranking battery and running the trolling motor batteries low I did the following:

First, I got an "on board" charger. You can get them to charge anywhere from 1 battery at a time to six batteries at a time depending on the model. The batteries on the boat were independent from each other so hooking it up was easy. After my first winter, I figured out that if I keep the two trolling motor batteries plugged into the wall, the charger would condition them and they wouldn't go dead. You can get an on board charger from any of the major fishing & hunting stores in town.

As far as the cranking battery, I kept having problems and I found out that when I troll, the engine doesn't turn fast enough to allow the alternator to charge the cranking battery while I'm running live wells, fish finders, radios, lights, etc. I bought an isolater from www.hellroaring.com and bought another deep cycle battery. The cranking battery runs the motor (starting and trim) and the deep cycle runs my accessories. The cranking has a priority to charge and once it hit 13.4 volts, the isolator kicks over and charges the deep cycle. If my cranking battery dies, the isolator switches and the deep cycle provides a boost. I keep the cranking battery connected to an "automatic charger" plugged in at home when not in use (when it is charged, the isolator allows juice to flow to the deep cycle).

In summary - 3 deep cycle batteries, 1 cranking battery, two chargers plugged into the wall when I'm at home. Xcel Energy loves me but I haven't had a problem since!
 

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Mr. Ed,
Looks like you have the battery problems under control. Like your idea of connecting all
but the motor and tilt to an extra battery. I think that you mean 13.4 volts instead of 13.4
amps.
 
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