Hopefully one of the guys that has the diagram for 24 hook up will post it. Basically you have 2 12 volt batteries, cable hooked from Positive of one battery to Neg of other battery. Your motor hot hooked to empty pos and motor ground to open Neg. You would need 2 leads of your charger, one set to each battery. Charger still see's each one as a 12 volt. I am assuming you have a 3 bank charger at this time. You could have one leg each to trolling batteries and one to cranking battery.
What is your other battery used for at this time?