Rgy, in answer to your questions:
1)One cup is probably enough, but you can use more if you need to. You just want to make sure as many bees as possible are coated.
Here's a video that outlines the process really well for your reference: Country Rubes' Powdered Sugar Movie Project_Final 4 10 10.wmv
Although I think she gets the reason sugar works wrong (she says it interferes with the varroa's grip when it's more that dusting encourages heavy grooming from the bees), this is a great detailed walkthrough of dusting and prepping a sticky board.
2) I assume you are using foundation in the brood boxes? How about in the supers? Often what happens is that the queen has very little room to lay drones down in the brood boxes because the foundation is uniformly worker-sized. If she wants to lay drones she will lay them in any area where she has room and the cells are larger, like honey supers or burr comb. It's definitely not too late for queens to be laying drones, though mine have reduced the number they are laying. No one knows exactly how a queen decides how many drones to lay and when, but my guess would be that means that the swarming season is not over yet in your neck of the woods.
The simplest thing to do about it is to leave your setup as it is. As you get into the fall, she will stop laying drones, those cells will clear out and the bees will store honey there instead. You just have to wait a while. If you are in a hurry to clear brood out of the supers, I can make some other suggestions.
3) I have just used commercial powdered sugar so far. Perhaps someone else can weigh in on where to buy powdered sugar without additives. Maybe a baker could tell you about their supplier? a cheaper alternative is to put granulated sugar in your blender and buzz it for a few seconds to make your own powdered sugar.