You can easily organize your PDFs in Papers by creating Lists or Smart Lists.
To create a list click on the gear icon next to All Papers.
From there you will need to select Create List or Create Smart List.
For Lists you simply name your List (you can also select if it needs to be nested into another list) and then drag and drop your PDFs.
Lists in Papers 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 Papers, the PDFs in that list will not be deleted. They will remain in your library.
For SmartLists you can create a query for your the list and your library will import all current and new entries that are part of the query into the list.
If you need help building your Lists or Smart Lists go ahead and email ReadCube Papers Support!