You can create and save annotations in the Research Notes field of the reference.
1. In your EndNote Web account, click the title of the reference you wish to annotate.
2. Click Show Empty Fields which is located in the top right of the screen.
3. Scroll down to Research Notes:
4. Click in the field to begin typing your annotation.
5. Click the Save button. (EndNote Web periodically saves for you.)
6. Below the Format Tab, select Bibliography.
7. If you have not added one of the annotated formats to your favorites, click "select favorites" and add any of the available forms, such as MLA-Annotated or APA-Annotated: 
8. Select that Annotated format as your preferred Bibliographic Style. Select the choices you want from the other drop-down menus, and Save.
View a brief Video Tutorial that will show you these steps. There is no audio. If you would like a larger video image, click here. (EL -- saved anywhere else? links broken)