Note: a brand new version of the ReadCube Papers desktop app for OS X and Windows will be available soon!
You can easily organize your PDFs in ReadCube Desktop (legacy) by creating lists.
To create a list click on Create a list and a new list will appear in the menu bar. Then simply drag and drop your PDFs into your new list.
Lists in ReadCube Desktop (legacy) behave like playlists, rather than folders. An article can exist in more than one list at a time. For instance, if you have a list of articles about cancer and another list of articles about mitosis, you can file the article "Mad2 over expression promotes aneuploidy and tumorigenesis in mice" in both lists, since it is relevant to both cancer and mitosis.
If you delete a list in ReadCube Desktop (legacy), the PDFs in that list will not be deleted. They will remain in your library.