You can easily organize your PDFs in ReadCube 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 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 overexpression 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, the PDFs in that list will not be deleted. They will remain in your library.