Be aware that annotations/notes added to PDFs in EndNote are only visible within the EndNote program.
PDF Handling Preferences
PDF Handling preferences allow you to define the automatic renaming process of PDF documents that you want to import to your EndNote library.
Go to Edit on the menu bar, select Preferences, then select PDF Handling.
Set Find full text Preferences
The Find Full Text command makes it possible to find the matching pdfs for references in your Endnote library. You can search for up to 250 records at a time.
Note: Endnote will only be able to locate PDFs with a DOI. Other PDFs will need to be downloaded and attached manually.
Setting Find full text references:
Preferences > URL & Links
Copy and Paste into ISI Base URL box: