I use the Raggtopp cleaner at the very beginning of the car wash. I use the protectant when most everything else is done. I don't know is this is the best way to do it, but it seems to work well for me.
You may find this video helpful:
Contrary to the practice commended in the video, I prefer to spray the protectant on a microfiber applicator and then apply it to the top. How do other AG members apply their convertible top protectants?