I have a 12 volt trolling motor and want to go to a 24 volt. What size wire do I use for this and how do I wire the Batteries?

Welcome aboard!

If you do a "search" I'm sure you will find some great info posted here.

I know this has been covered in depth (no pun intended) before.

6 gauge wire will be sufficient, and wire the batteries in parallel; pos to neg, hook tm up to one battery's positive, the other battery's negative.

Just to be clear is this a straight 24volt or a 12/24? How many holes on your recepticle on the boat now? How many wires run from the battery area to the recepticle now? Do you want to use a "mount in the boat" charger or a universal battery charger? Lots of ways to do this based on your answers.

Just thought of 2 more questions. Do you have 2 trolling motor batterys in the boat? If not, do you have room for a second one?

I have bought 2 batteries, on-board charger 2-bank 24volt and am fixing to purchase 24 volt motorguide trolling motor. I will have to wire the batteries together, which I understand how to now and next will have to run wire from batteries to front of boat for trolling motor plug-in. Do I need breaker or fuses in between batteries and trolling motor? 6-Guage wire should be good enough??

minn kota recommends a 50 amp circuit breaker on the hot side. not running one will void your warranty.  Don't know what motor guide suggests....

six gauge will be plenty fine.

They make circuit breakers that attach under your wingnuts on the positive post of your batteries, get one for each battery. The earlier suggested 50 amp will be plenty. If the breaker ever pops there is a small reset button on each breaker.