It seems like the PURPOSE of this technology (sorry, I am frustrated that I have spent time trying to understand this product) is to add my commentary to files. For example, I am an academic, and read a lot of pdf articles. I would like to attach notes about that article to the article. Is that impossible?
I often do ‘attach’ notes to PDF documents. There are two ways to do this:
 One can enter notes and comments in the document’s Info panel. I often do that.
 But for many purposes I prefer creating a new rich text note and writing notes and comments in that document. I link it to the relevant PDF by giving it the same name (with an extension such as ‘note 1’, perhaps. By doing that, if I search for the name of the PDF I’ll also pull up all the notes associated with it.
And I’ll hyperlink my notes documents to the relevant PDF – and perhaps also to other notes and/or other documents. So it’s possible to create quite rich ‘attachments’ to a PDF.
Bill, while this works for you, it is definitely not intuitive for most people, and especially beginners.
This is one of those “DEVONthink Academic” features that I think would be very useful. And it is one of those usages that highlight the benefit of dynamic integration w/ a bibliographic program like Bookends ([a] automatic and live indexing and updating of all the fields of the bibliographic software’s entries, [b] links to existing PDF’s in DT’s database, and [c] the connection of groups of notes to both the PDF, and the bibliographic entries from Bookends).
But barring that, what would be best would be some way of easily and transparently attaching not just a single note (through linking), but a whole set of notes to (1) a PDF that’s in the DT database, or (2) to another entry (like a sheets entry for each bibliographic reference imported through bibtex from Bookends, for example).
I think a lot of people come to DT – considering it’s probably the premier consumer PDF managment software on the market (amongst other things) – thinking that this should be a given. The comments field is just not inclined for this. And as the poster makes clear above, those coming from academic backgrounds especially need this.