I’m surprised to hear about these difficulties with Sente—I was under the impression that it handles notes and annotations expertly. A major weakness of Bookends, in fact, is that it does not support Applescript. Nonetheless, the DT developers somehow pulled out a template-script combination which produces a new RTF note with the following information:
— Title of the reference selected in Bookends
— Author of the currently selected reference
— Year
— Keywords
Additional space for typing notes is provided by the template. Also, the URL of the note is set to the “bookends://” URL of the corresponding reference.
All in all, it works wonderfully.
If you are able to read Applescript, and also comfortable with creating custom bibliographic styles in Bookends, you will have no difficulties automatically importing any fields you want (e.g. notes).