Don't assume you can just take alligator clips off the existing wires and add more wire with a good butt connector. That may work, it depends what gauge wire originally comes on the Minn Kota, quite possible that extended length is not safe at that wire size and you need to replace the entire lenghth with a heavier gauge wire.
Here's a quick, clean solution: from the battery back to a convenient place the existing Minn Kota wires reach run heavy gauge wire, that can end at nice posts the alligator clips can clamp onto. On battery end you can crimp regular battery lugs, makes for a clean installation