There are two ways to annotate articles or take notes in EndNote Desktop:
Use the "research notes" feature. Select the citation you wish to add notes to, click "edit," and locate to the "research notes" field. This is different than the "notes" field, which usually contains citation information. From here, you can add any notes you wish. If you choose to export an annotated bibliography, these research notes will show up as annotations. Almost all other styles will exclude them automatically.
Annotate directly onto the imported PDF of the article. Select the citation you wish to annotate, go to the PDF, and use the features in the top left-hand corner of the PDF to add comments, highlight phrases/sections, etc. Please note that this method requires you to either import PDFs manually or use the "find full-text" feature, which auto imports the PDFs for you (instructions on find full-text here).
