You can’t organize files/folders from the WMD app, or specify what folder to upload to. This is a MAJOR shortcoming IMO. At least on the PC side, you can organize all you want, and the WMD app will be able to access all the new files/folders.
Of the four folders you listed, only the Upload folder seems to have a purpose. This is the giant pool where anything and everything you upload from your device goes. I guess the other three folders are just suggestions of where to put your content, though your content will be found no matter where it is. But don’t bother deleting these folders if you don’t use them, because the app will just uselessly recreate them.
