Design opinions and a reader question
Either way works fine.
Here's the difference. If i am understanding, you are building a rnaf wing (4 mil bottom 2 mil top).
you can run the 4 mil on the bottom either direction. For a really flat bottomed airfoil, you run the 4 mil flutes chordwise, add an aileron on top of it, and then glue the 2 mil to the aileron piece, and you get a very flat bottomed wing.
If you want a more semisymmetrical wing, run the flutes on the bottom spanwise, and cut the aileron out of the bottom piece of coro.
As far as differences go, there's not much, the single 4 mil bottom and aileron will fly inverted a little better. Besides that, there's not much diffeence in the two.