With two batteries, you should charge them separate if they were used separately as one could be used up more than the other... I have found that with my fishing/electric motor the battery's never charge up as fully together as separately... JMO Unless I charge them up with one charger - on one battery and the other on the + on the other battery with both batteries hooked together with separate cables in parallel?... Don't really know if that makes sense but... It works well in that application.

.................................. +).....(-' neg battery charger
positive battery charger '+(.....) -