Re: two battery hookup
You need to determine for sure what you have and to be a little more clear before we can make any recommendations. Everything on a small boat runs on 12V with the exception of some trolling motors. Some of those run on 12V, some run on 24V and some run on either 12V OR 24V. I posted three diagrams in the link below. Go there to help determine what you have.
http://forums.iboats.com/showthread.php?t=204320
If your trolling motor runs on 12 OR 24V it will have a switch either on the motor or on a separate panel at the front of the boat. If it doesn't have this switch, you have either a 12V motor or its a 24V only motor. If its a 24V ONLY motor and you are using only one battery you are getting very poor performance and roughly half the power out of the motor.
If you will run two batteries, I suggest you use one for the engine and all accessories except the troller. Use the other battery for it. If you simply parallel the two batteries and wire everything to them, you run the risk of running down both batteries and the engine won't start. Next, you need to determine how you will charge the trolling motor battery. The engine will not do that as it simply doesn't have enough output to top off a deeply discharged battery. You have to run wide open for hours. The best bet is to simply leave the engine and accessories on the start battery. Accessories don't take much power. Wire the troller to the other battery. Use a hand held charger at the dock to charge it or install an on-board charger that you leave in the boat and plug in at the dock.