John,
If your boat is pre-rigged for a 24 volt motor just hook the batteries as instructed in the owner's manual.
Otherwise, wire the batteries in series. This is linking the two batteries with one negative and one positive. This will leave a negative and positive terminal open, to which you will connect the appropriat leads from the trolling motor.
Hope this helps.
Best of fishing,
Dan
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Dan Galusha : Bassin' USA Prostaff : Illinois