A typical charger has two leads, a black/negative and red/positive. If this is your case, its likely that its a 12/24/36 volt charger but if you want to be sure connecting a simple volt meter between the leads will tell you for sure if there is not a voltage selector switch. Set your meter on Vdc and choose a range above the expected voltage. Most meters have a 20 vdc setting. This would be what you would choose for a 12volt output. if it does not show anything on the meter go to a higher setting say 200vdc. Connect your meter lead across the charger leads and if its a 12 volt charger you should see in the range of 14.5vdc. If it is a 24volt charger you will see roughtly 29Vdc. A charger will always be a few volts higher than the load it is charging. Which means if what you wrote above about 24 volts means a 24volt charger (and your sure) you would only charge your 2 12volt batteries together. Two 12volt batteries wired in series produce a 24volt supply. If you are not sure about if they are already wired in series, you will see a positive lead, (likely red) from your trolling motor going to one batteries postive terminals. The negative terminal on that batter will be tied with a short jump to the positive terminal on the second batter, and finally the second batteries negative terminal will be connected to a black or negative lead of your trolling motor. You will connect the battery charger between the postive lead of the first batter and the negative lead of the second battery. The same connections your trolling motor makes. You should be able to safely charge a 24volt battery supply in your 40amp mode. Watch your leads for excessive heat and check repeatedly. If its not a smart charger, I would remove the batteries and put them on the ground outside for the first go round. Never put a 24volt charger across a single 12 battery. guaranteed be a hazard. Finally buy a six pack for a friend that knows it better than you. There is no substitute for experience.
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