You can separate the two batteries, and then parallel the two charger outputs and connect them to one battery and charge at 40 amps. But why???? You then must repeat the process for the other battery so total charge time is still double. There is no advantage in doing that. Read on!~
You do NOT charge them in series. Forget series because you have a 12 volt system. The batteries are in parallel, so connect the two sets of outputs from the charger in parallel and then to either of the two batteries. You will have 40 amps into the two battery bank even though the outputs are connected to only one to the batteries. An alternate method is to again parallel the two sets of outputs and connect the positive pair to the POS terminal of one battery and the NEG pair to the NEG terminal of the other battery. Understand that two supposedly identical batteries are not really identical in capacity. Close when they are new but not perfectly identical. As soon as you parallel them, those two batteries will begin to equalize. During the discharge process (running the trolling motor) one battery may lose capacity at a greater rate than the other. During the charging process the opposite happens, The most deeply discharged battery will likely charge at a greater rate than the other until they equalize at which point once again, the charger is looking at one giant battery rather than two smaller separate batteries.
If you thought you could separate the two batteries and use one set of outputs on each battery, or actually configure them in series and charge at 24 volts, that is possible but it is of no value. You have a maximum output of 20 amps per output. So here are the possibilities:
1) Batteries left in parallel: Both charger outputs paralleled provides 40 amps into the bank.
2) Batteries separated: One charger output goes to each battery providing 20 amps to each battery.
3) Series connect the batteries in a 24 volt configuration. Again, one pair of outputs to each battery provides 20 amps to each battery.
4) Series connect the batteries in a 24 volt configuration: Connect the two sets of charger outputs in series and then connect output 1 POS to 24 volts POS. Connect 24 volts NEG to the NEG 24 terminal.
Configurations 2, 3, and 4 are no advantage to you and add a great deal of complexity to the wiring. There is no free lunch with this stuff. You have 40 amps max that must service 2 batteries. Why complicate the setup and introduce all sorts of points of failure only to accomplish the same thing as #1. Use configuration #1 and go fishing. Did you also know that the safe charge "rate" for most batteries is 20% of its capacity. Therefore a 100A battery should not be charged at more than a 20A rate.
