My 2 1/2 cents worth....

I also use 2S LiPos in my airborne set-ups and regulate the voltage to 6 volts.

The batteries come with the balance jack already installed so I tend to use the balancer. Not every time but fairly often. BUT I never charge in the plane. I have mine set-up so the battery sits up just under the canopy so it's simple to reach and remove/reinstall. Just a little forethought is all it takes and I'm sure you can do that too! Most that use LiPos in their airborne set-ups do that.

One other thing I often do is to check voltage after the second and fourth flights. The discharge rate has been extremely consistent so I know within .03-.05 volts how much drop each flight produces. I run my airborne and CDI from the same battery and the 2000 ma gets me 75 minutes of flight time or 5x15 flights