My uneducated guess is that batteries should be of the same capacity and cell condition whether two 6-volts in series or two 12 volts in parallel for best charging and performance. I would even try to use the same brand batteries.
With RC model electric power system batteries, we use sophisticated balancing chargers that try to equalize the charge levels/voltage of all separate cells. We consider a battery pack no longer unusable when one or more cells stay at much lower voltage despite the balancing charger's efforts to bring all cells up to the same voltage/charge level. I use two 3-cell 2200mah li-poly battery packs in series to power the electric motor in my 6-foot wingspan J-3 Cub model, same as using a single 3-cell 4400mah battery pack.