I have an 16 foot bass boat and I've come across a great smallmouth fishery. It's a river and it's tidal water so if I'm fishing on an incoming or outgoing tide, I'm fighting current most of the time.

I have 2 trolling motor batteries. Both are less than a year old but are different sizes.

Would I get more time out of them if they are rigged together or seperately???

I don't know what it's called but I currently have the batteries rigged together but staying 12 volt. In other words, positive to positive, negetive to negative.

I have a 40 lb Minn Kota and I usually stay out fishing all day if I can or what usually happens is the batteries give out long before I do.

Any suggestions????

Anyway, just wondering if I'd be better off running on one battery at a time or both at the same time.

           Thanks

I assume your motor is a 12 volt motor.  You will get longer run time by connecting the batteries in parallel over running one battery, then switching to the other.  This is because the heavier the load on a battery, the lower the amp hour rating.  By connecting the batteries in parallel, you are basically cutting the amp load in half on each battery, therefor increasing the amp hour capacity over using just one battery.  Being different size batteries, it's not going to actually half the load per battery but it will still be much better than running on one at the time.  

If running a 24V TM on two different size batteries connected in series, you will damage the batteries so don't try that one.  In series they must be the same size, type and age.

There you go, anything else we can help you with. ;D

I suggest that you find out the reserve amps of your batteries and next time you buy some get more reserve capacity.  You need 180 or more reserve amps, especially with a 12 v trolling motor.