I am not sure I totaly understand all your question. Let me tell you how it should be set up and mayabe you can catch on. If you have two elevator servos and want to use flaps with aileron than you need to make a decision. With a 5 channel set up you will have to do one of two things. Either use a reverse Y harnes on the two elevator servos and plug them into one channel and have your aile servos on two sepperate channels. Or use a normal Y harnes on the two AILE servos and use a different channel for each ELEV servo.
This is assuming you have two servos for the elevators and one for each aileron. I would use not set up this plane for flaps. The j-3 Cubs land so slowly that flaps are not really needed. So I would mix the elev servos together on the radio and use one channel for each. Then use a Y to plug both aile servos into.
If your set up is different from what I have described please let me know. I don't have this plane and I am not sure how many servos you are using.

David