I attached the wings to the fuselage with the flaps and ailerons attached, since I had already rigged them in the wing stand. But, each member of my group of 4 guys had experience installing RV-14(A) wings previously, so I felt comfortable leaving them on.
If I were to do it myself or with only one other person, I'd keep the wings as light and nimble as possible and thus would remove the flaps and ailerons.
_Alex