There are, as usual, many different techniques to use in powdered sugar dusting. Some people do each and every super on the top bars, some people say just doing the very top super is enough and the sugar falls down enough to cover the bees.
I think it depends on how infested the hive is. I am having major trouble with mites right now, and so I am doing the sugar dusting (using a flour sifter) on each and every super (except the top honey one). I sift the powdered sugar over the top bars and brush the sugar down off the frames. The bees really hate it and I do smoke them to calm them down, but I have noticed that they recover really, really fast. They start to forage and do orientation flights shortly after. It really seems to be working, as I am knocking off many, many mites.
Now I have heard from some beekeepers that they only dust the very top super and brush it down. I don't know. Maybe this would be better when the weather is cooler, as you do not have to expose all the supers to the cooler weather. I feel that I do a better job when I do each super separately, as the frames may not be completely lined up in each super. I seem to get more mites when I do each super separately. It is a big job, but very rewarding to me to know I am not using any chemicals in my hives.
I am going to try to regress to small cells slowly, as many organic beekeepers have done on this forum, and hopefully get rid of this horrible problem of the mites.
Have a great day