Since you have a 12 volt Minnkota, you do not need to put everything back as it was, and without the wiring diagram for the boat it would require input from someone who has the same boat who can take pictures for you. Otherwise it's a guessing game. Here is what I can tell you for sure.
1) You have two deep cycle batteries because they were required for operation of a 24 volt motor (which yours is not). They would also be required if you were to have a motor that ran off of 12 OR 24 volts (also which you do not have).
2) Each of those batteries has a pair of wires going up to the control panel at the bow. This is simply two totally separate 12 volt circuits.
3) The 12/24/RUN/Charge switch was an attempt to make charging the trolling motor batteries simple by plugging the output of a single 12 volt charger into the trolling motor receptacle, thus making it unnecessary to attach it to the batteries. Nice, but an overly complicated system since you have an on-board charger that only needs to be plugged into 120V AC and all three batteries get charged.
Here is my recommendation,
1) To avoid screwing up the resale value of your boat, DO NOT remove any switch or remove any wiring.
2) Install the new switch but leave the wiring as you found it.
3) You have the perfect setup for a 12 volt motor in that you have two 12 volt batteries. That gives you the following options:
a) Wire only one to the trolling motor receptacle so the motor runs from just one battery.
b) Wire both batteries in PARALLEL so voltage remains at 12 volts but you essentially double the run time.
c) Do "b" above but rather than permanently wiring both batteries use a dual battery switch (Perko is just one brand) to select which battery you prefer to run from. This method allows you to use battery #1, battery #2 or both. These switches are available right here on IBoats for about $40 give or take a little.
4) At the trolling motor receptacle, all you need is one 12 volt circuit using any two of the four terminals.
5) Wire the plug on your trolling motor so the red and black in the plug match with the +12 and ground terminals in the receptacle.
Wiring the batteries with a switch is a matter of connecting BAT #1 POS to BAT #1 on the switch. BAT #2 POS goes to BAT #2 on the switch. COM gets wired to the receptacle at the bow. Use one of the wires already in place -- preferably the red one. Connect the NEG terminal on both batteries together and then connect the black wire going to the receptacle to the NEG terminal on either of the batteries (use the black wire already in place). Plug in the motor and go fishing.
To wire the batteries in parallel, simply connect them POS to POS and NEG to NEG. Then use one pair of the four wires going up front as the 12 volt feed to the receptacle. This is not the best approach since batteries permanently in parallel can create issues in that a weaker battery can draw down the stronger battery until they equalize. The Perko Dual Battery switch eliminates that issue.
When this is all done, connect each of the three on-board charger outputs to each of the three batteries. Always charge the batteries after every trip. Don't leave them in a discharged state.
