Right now I have two main sections of decks with a bunch of subfolders in each:
Section One is my 60-card decks and only contains all the pre-made decks (i.e. PW Decks, Duel Decks, etc) that I've purchased over the years that I wanted to maintain deck lists for in the event I ever want to reconstruct them. These decks obviously don't get moved around much at all.
Section Two for me is titled EDH as I only play EDH at this time. I have four sub folders: BUILT / IN WORK / IDEAS / REQ PURCHASE. As I construct or modify my decks, they get moved from folder to folder. I'm constantly looking for ways to improve my decks and regularly have a new idea or two brewing, so I'm moving decks around once or twice a week there.
If I collapse all the folders, I can manage to move a deck between folders with relative ease, but it's definitely a pain once you get up to 15-20 decks in a single folder as it starts taking up screen space and drag-and-drop because more difficult. A "Move to folder..." option in the deck tools or someplace similar would make it easier for folks with a lot of decks and/or folders.
Just wanted to add my two cents.