Assuming that the intended color is to be white (which is pretty common for this type of aircaft), the suggested procedure is to first cover the control surfaces with film and thereafter apply the strips using CA.
For any color other than white, I would still cover the control surfaces first. The color of the strips would then have to be matched. If the correct color paint can be obtained, this would be the best method of coloring the strips before gluing them down to the surface.
Using film on the strips for color, while not impossible, would be a very tedious process, to say the least.
Since the strips are styrene plastic and therefore sensitive to heat, they may be affected by the temperatures necessary to apply film.
Be warned that whether you choose the most successful method of installing the corrugations or you're going to experiment with your own technique, it's a slow and painstaking process, but the results can be very rewarding.
Although it goes without saying, check on the real aircraft for the quantity and exact positioning of the strips. I've seen gross inaccuracies in this area even on elaborate giant scale ARFs.
I am personally not using film, but still prefinishing the control surfaces prior to adding corrugations and I can say that these styrene strips do work quite well!