EndNote can be set up to import from a selected folder on your computer automatically:
PDFs added to the folder selected will automatically import to an Imported References group in EndNote. The Imported References group is a temporary group that is replaced each time you import another set of references. It is removed when you exit EndNote, although the references remain in the library. It is advisable to move your imported references into a Group, or they will remain in the Unfiled group.
Bibliographic details will be entered automatically only where there is sufficient metadata in the PDF for EndNote to be able to identify the item. Where bibliographic details are not entered, there are a couple of options to consider:
Import a journal article PDF and create an associated reference. (1 min 32 secs).