How to decide what size trolling motor  battery to buy ! I have a 15'3" Skeeter Bass boat with a 43lbs thrust motor guide trolling motor. I need a battery that will run trolling motor for at least 8 hour bass tournaments. I spend more time trolling than I do running. Which Battery and what size ?

Something with high reserve capacity.   Maybe even 2 wired parallel. 

Measure your area and get the biggest series group that will fit in the hole and like said high RC 200+.

These are on sale right now, and are a great bargain, if you need cranking ability also, it's a steel!!

http://www.vmaxtanks.com/MR127-100-Deep-Cycle-High-Performance-AGM-Battery_p_24.html

But if you want better,, check the one below. I just bought this one last week on sale for close to this price. Do some check'n and be assured these are some of the toughest batteries out their, with better runtimes due to more expensive alloys!! Yes it is a solar backup, which is better at deep cycling but not built for cranking, so if you are dedicating it trolling motor only and strictly deep cycle work with your trolling motor, they are actually better. If you call and are a first time buyer, they will work with you and check around on price, they will match anyones current price on the same battery. I found one on Amazon, called Customer Service, and got the sale price, with a discount on that, and free shipping. Vmax maxtanks will get all my battery business from now on!!

http://www.vmaxtanks.com/SLR125-AGM-Solar-Battery-_p_38.html

Check their runtimes on your trolling motors here. 

https://dl.dropboxusercontent.com/spa/wccow3cq8q8hrus/trolling_calc2014/trolling_calc2014.htm

I will highly recommend these Batteries for the long haul, and in the the future they will be a price savings to boot!!

The 3 most common sizes found in boats are the group 24, 27 and 31. 24 is the smallest, and 31 is the biggest. A lot of it depends on what you can fit in your storage. For instance, with my boat for my 24 volt tm I've got to run two 24's because I can't fit 2 27's in the back. I've never had an issue going well over 8 hours with a set of 24's though. For your situation, I'd be looking at running 2 batteries in parallel. Try to squeak 27's in and 24's if you can't. 

I am using a group 29 interstate with a RC of 210. It runs my 55 lb. Minn Kota Traxxis all day with no issues at all. The battery set me back $125. It is a 63 lb beast though.

12 or 24 volt trolling motor?

What type of charger do you have?

Tom