Bookends or DTP as center of workflow?

Hello, new member here. :-)

I'm currently saving my pennies for a replacement mac laptop, and am also plotting for a good academic research workflow.

My pencil and paper understanding of workflow is: read document, mark it up, reread, make notecards. (I'll ignore actually producing a paper for now.)

"Everyone" says DTP (especially with OCR) is wonderful. But I'm stuck trying to envision how to do notecards. Bookends allows you to associate any sort of file with a bibliographic record. The original PDF and any RTF or TXT "notecard" files you wrote yourself.

DTP does not allow you to link materials with a bibliographic record(?). But I think putting my "notecards" with single thoughts and small excerpts (as well as full PDFs) into DTP will help me write papers better, especially over time.

Or should I associate the notes with Bookends, and just link to them from DTP, instead of creating them within DTP?

Obviously I'm fishing for workflow suggestions here. I just want a great notetaking and organization method that ties into Bibliographic info.

Thanks,
Phil