Assuming house batteries are still in place, house converter/battery charger isn't adequate? Are you Winterizing? Do you wish to trickle charge for the Winter? If so, parking arrangements or where the batteries will be located? What kind of RV? Just asking for basic info?
A very basic answer to a very basic question is yes. If the batteries are to be in a stored state, they should be disconnected from the RV. To cut any phantom voltage draw. Assuming the batteries are wired in parallel, hot (red) clamp from the charger to the positive side of one battery. Negative (black) clamp from the charger to the negative terminal of the other battery. This way, the charger charges them both as "one battery". And equally, if both batteries are of equal group and condition. A bunch of variations are involved here. Maybe more info is in order for a better answer.
Depending on the type of battery issue you are talking about, and what you are trying to accomplish, there are a whole slew of possible answers to protect you and your RV and do it right!