Major Mark posted this link earlier, it is the clearest explanation I have seen. Assuming your charger is 12 volt on both banks, I think Figure 7 shows how you would do it.
IF it's a 2 bank/12 volt charger built for 12 volts batteries, it is 12 volts PER bank. Look at figure #7. Just vision instead of 2 chargers, you have one charger with 2 separate sets of leads paired together(one pos, one neg per set). One positive and one negative goes to each battery individually.
i wondered about connecting a 2 bank charger to a 24 volt system i though the jumper between the two batteries would cause problems with the charger but was assured by a sales guy at bps that the jumper had no berring on the charger.