Yeah, from one battery to the other they should be fairly balanced as long as the connections to each are equally good. As far as the cells inside each batt, balancing those is the BMS's job although i've heard some BMS's balance so slowly that they can't accomplish it in the time available when the batteries are constantly in use. So inside the batt could be an issue but even so, it's probably a red herring to bring it up unless the charge controller is actually in communication with the bms's in the first place.