I would like to know, if possible, how to wire a third battery to a 24 volt trolling motor so to increase the amount of charge.  I have a friend that has his cranking battery directly connected to one of his trolling motor batteries so he can charge two batteries while the big motor is running.  

Right now I have added a third battery to my back compartment and would like to know how to connect it to the other batteries without throwing 36 volts to the trolling motor.

Check out this link. There are some helpful diagrams.

http://www.boatfix.com/how/Ele2.html

Also, do a search for "battery isolator."

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Two batteries parallel and then those two in series to the third. That will increase amp hour for the parallel batteries but I don't know about the disparity of the setup in series. It is generally recommended that batteries in a pack have the same capacity, both in voltage and amp hours.