I'm almost certain you need to charge/balance each 3s pack seperately, or two cells will short through the balance taps... In other words, the pack needs to have 4 main connectors on it, and two balancers when charging. To run in 6s mode just connect the two short leads (red/black) together and the long leads to the ESC, or vice versa. I am assuming one pack has a LONG RED and a SHORT BLACK lead, and the other has a LONG BLACK and a SHORT RED lead. You may want to test with a meter to confirm this.
I'm a bit tired so I could be wrong- another good reason for you to use a meter and test/label the leads.
