in my boat i have the cranking battery going to gps,radio and my talon,this way when the boat in running the battery will stay charged.and have the trolling motor by itself,because if you have everything hooked up on the trolling motor batteries they are not going to last long with everything running.hope this helps

ditto to n s 21

I am similar to the other guys. But, I have my cranking battery going to the engine alone. My VHF, stereo, depth finder, and chart plotter/GPS on another. This second battery still receives a trickle while the engine is running.
My trolling motor resides on an independent battery.

Your cranking battery is being charged while underway by the outboard's alternator just enough to keep it at a minumum charge. Its best to also run your accessories off the same battery since the drain is very little and the alternator can keep up with it. Only use your 2 trolling motor batteries dedicated for your TM, make sure to completely recharge after every day's use. This prevents any 12V voltage leaks through accessories that would otherwise slowly drain your TM batteries and ruin a good day fishing. This is from 30+ years experience with boat electrical systems. A tip- run a 6 gauge jumper cable between all your negative battery posts (including the cranking battery) to minimize voltage leaks. This will not affect your 24V TM battery hookup or cranking battery operation.

I have 2 batterys in the back. 1 for motor and a spare.. How do i hook up two batterys to the motor? Also will the motor charge 2 batteries while running?

Connect the 2 positives & 2 negitives together & they will work like one big 12v battery.
With that said, the best thing to do is use a switch. Then you can select Bat #1, Bat #2 or both. Then you will have a true back-up.

Nick, I have a 36-volt MotorGuide, and run a total of three batteries. I have them all linked, and the accessories connected to the cranking battery.

The 36-volt motor pulls such a small load that it works like a charm.

I've never had a problem, even when fishing in strong wind and tides. The system is like the Ever Ready bunny: It just keeps on going.

Not sure if the same would hold on a 24-volt system, but it works for me. And it holds the weight of the entire system down, along with the cost of batteries.

I agree. I have a 24 volt trolling motor. The two batteries up front are dedicated for that pupose alone and have a mounted trickle charger that I plug in after every use. The battery in the back of the boat is for cranking, GPS, DF/FF, bilge pump and baitwell pump. I always have enough power with the 24 volt trolling motor system and my motor cranks everytime. The twoo batteries up front also evenly disperse the weight. When I had an offshore boat I had two batteries in the back and had a switch where I could alternate use or charge both when running. Hope this helps.

Your outboard alternator will not keep 2 - 12V batteries charged sufficiently. Considering the length of time your outboard is actually running during a day's fishing, its not long enough to keep both batteries charged. Its best to use only 1 battery for cranking, but it should be the highest cranking amps you can find. Don't use a deep cycle trolling motor battery for a cranking battery.