Re: 24 volt or 12 volt system?
This is what i have:
there are the main battery cables that hook up on the battery posts for the motor. There are separate cables there that just have ends to connect to a bolt size connection on the battery with a wing nut.
I assume the trolling motor needs 24 volts. so, those leads that connect on the smaller battery connection need to connect to which battery? i need to connect two batteries together only for the trolling motor?
You need a primer on how all of this works. The first thing to keep in mind is that all boat batteries are 12 volts. Your main motor, the 90hp Johnson, requires one 12v battery to start...exactly like your car. That battery is typically located in the back of the boat near the big motor. That battery is designed to start your big motor and run your accessories but should be kept well-charged. Your big motor has an alternator (just like your car) that keeps that battery charged when the big motor is running - but only at speed, not at idle.
Unlike your big motor that just needs a 12v battery to start, the trolling motor actually runs off of the battery. Therefore your trolling motor requires a different type of battery, called a deep-cycle battery. Deep cycles are made to be run down to empty and then recharged. If you have a 24v trolling motor then it needs two deep-cycle batteries just for itself. Those batteries need to be connected in series. You'll connect the negative cable that goes to your trolling motor to the negative post of one deep-cycle battery, and the positive cable to the positive post of the second deep-cycle battery. Then you run an 8-guage battery cable from the positive post of the first deep-cycle to the negative post of the second deep-cycle. This is how a 24v system runs.
If you only have a 12v trolling motor, you have the option of running it off either one 12v batteries or two 12v batteries. If you run it off of two 12v batteries, you connect them in parallel so that it's like you have a big 12v battery that lasts twice as long. To do this, you connect the trolling motor cables to the positive and negative terminal of one battery. Then you run 8-guage cables from the positive terminal of the second battery to the positive of the first battery, and the negative terminal of the second battery to the negative of the first battery.
So if you do indeed have a 24v trolling motor, you'll need three batteries in your boat. The first battery starts your main motor and likely runs your electronics (depth finder, GPS, lights, bilge pump, etc.). The other two batteries will be connected in series to create 24 volts for your trolling motor.
Hopefully this helps.
p.s. Since your trolling motor doesn't have an alternator like your big motor, you'll need to charge the deep-cycle batteries used to run the trolling motor. You can buy a battery charger and charge each of the deep cycle batteries after use. These days, many people use bank chargers. You would need a 2 bank charger for your 2 batteries. This essentially allows you to just "plug in" your bank charger and it will take care of all the charging.