Mickey,
I think that if you rig the ailerons correctly, they will be in the same place on the plane that they're in when they are locked with the jig. (Unless you intend to play aero games & rig the ailerons to cause washout, or something similar...)
I agree with Norman; when I did mine, the 1st one came out matching the aileron perfectly and the other (when I 1st drilled it to the wing) was way off. I obviously wasn't watching what I was doing on the 2nd one. I took out all the clecos, and was able to move the tip into alignment with the aileron. The leading edge still fit perfectly, and the 1st set of holes I drilled moved a significant fraction of an inch; far enough that I was able to redrill without worrying about hole-to-hole edge distance.
Charlie