Pritch, look at the wiring setup I did with my battery switch, VSR and buss's, http://www.pontoonstuff.com/forum/forum_posts.asp?TID=3724. I think it'll help with your wiring idea. My trolling motor is running a 10ga wire from the front to the console and although I do have a battery specifically for the trolling motor there (on a separate charger), I could have just as easily attached it to the positive and ground buss bars there to get its juice from the rear accessory battery. I ran an 8ga from the rear accessory battery (could have done it from the rear buss bar's) to the console buss bar's, total of 15ft. That way you wouldn't have to increase (which was impossilbe in my case) the wire size from the trolling motor to the battery as I stayed with the max 10ga that was already on the trolling motor. I assume you already know how to wire the 2 6volt batterise to get 12volts, but I'll post the pic for others considering something like this.

This is the system I put on my boat, the switch and VSR are both small and compact, easy to mount out of the way or wherever you want it. http://www.ezacdc.com/Scripts/prodView.asp?idproduct=109