1) Open the PDF you attached to a reference in Endnote.
2) Click the icon for Annotate Tool bar on the left top corner for more options.
3) Select the text in the PDF and choose different icon under the Annotate Tool bar for different annotation e.g.: Sticky note (for notes or comments) Highlight (for highlighting some text in different color) Underline (for underlining the selected text) Strikethrough (for crossing out the text)
4) Close the PDF andSavethe changes
Here is a video for adding the annotations to your PDF in Endnote: