Vagent,

I can't say about the JR radio, but my Hitec flash5X has the same kind of setup Ch1 and 5 for flaperons. On mine I have to adjust the ch1 and the ch5 endpoints as they each affect a different servo. Once I get the endpoints tweaked so that the throws are the same for ailerons, then I just set the flaperon settings as a percent of current throw which affects both servos equally.
Hope this helps some.

Duke


edited for typing dumb-thumb....