Putting it back the way it was may not be a good idea which is why the prior owner did what he did. To fix this we need to know if your trolling motor is a 12 volt, 24 volt, or a combo 12/24V model. I will assume it is a 24 volt model or perhaps a 12/24 since you mentioned troller "batteries" (meaning more than one). However, two batteries in parallel still provides 12 volts but doubles the run time so you may have a 12 volt motor. See where this is going???? One thing is for certain, you cannot have a combo 12/24 setup if there are only two wires running from the batteries to the motor. 12 volt systems will be a two wire setup. 24 volt systems can be either two or four wire systems. Combo 12/24 systems can be three or four wire systems. That's about all we do for you until we get more detailed information on what your motor is, what the current wiring scheme is, and what you intend to accomplish with this rewire.