One suggestion, while charging keep be aware of the pack temps. If one pack is heating up more/quicker than the other, this would indicate a mismatch.

Certainly as cell counts go up there is more possibility of problems, 6 cells will help but not eliminate that, not until you go to single cells. But you are already discharging together, so no way to completely avoid this issue. Which suggests another bit of advice: Don't run the vehicle all the way down, stop as soon as you detect loss of power. Other wise weaker cells might get reversed.