3 bank charger?

[mrex]

I am confused just purchased a 36 volt trolling motor got it hooked up and everything is working correctly. Also just purchased a 3 bank charger read directions and looked up a few sites on internet.

Appears I just hook up positive to positive and neg to neg on the 3 wires coming off of charger to batterys.

I do not understand how it seperates the batterys voltage since they are connected togather. Have not turned anything on yet do not want to fry everything. Am I missing something or is this as simple as I do not understand how charger works seems to me the 36 volts would fry a 12 volt charger if wires are still hooked up.