Note: a brand new version of the ReadCube Papers desktop app for OS X and Windows will be available soon!
No matter how you get your articles or where they end up, ReadCube Papers can find them! Just set the folders you'd like ReadCube to monitor in the Preferences section of the desktop app, and any new PDFs in those folders will be imported automatically.
To set up your watch folders, go to the preferences tab - the gear icon in the bottom left corner of the desktop app.
From there, select the ReadCube Pro tab.
Select the folders you would like ReadCube Papers to automatically synchronize. Remember, we will sync every PDF that hits this folder, so it may not be ideal to set a general folder like your "Download" folder.