A new option in EndNote X8 is to automatically import PDFs from a specific folder that you select. Whenever you download or copy a PDF file into this folder, EndNote will attempt to automatically import it and create a reference.
1. Create the download folder to use if it doesn't already exist
2. Click Edit ► Preferences
3. Select the PDF Handling section on the left
4. Click in the Enable automatic importing checkbox
5. Click on Select Folder and browse to and select the folder to use
6. Click OK to save
To automatically rename imported PDFs with a more identifiable name (e.g. Smith2016.pdf instead of a download name of 4321dxtrn6789.pdf).
1. Click Edit ► Preferences
2. Select the PDF handling section on the left
3. Select the pattern that will determine how your PDF files are renamed
4. Click OK to save
Note: imported PDFs will be listed in a group called Imported References.