I agree that Rachel Leow’s series is a very good read but Devonthink has also moved on a lot from the time of the series and a lot of things she does manually in her post can be done much more efficiently. This post might provide some ideas : [url]Annotation Pane (Annotation with Links, Notes, Tags v3)]
Like Christopher I am a big proponent of regular review of one’s notes and the use of replicants. Working from either the tag view or a chronology view of annotations and source documents I replicate the documents into a folder structure akin to a table of contents for what I am writing. That way the relevant passages of my source material are already structured into the topics I am likely to be writing about. I also like to write up scraps of material as I go along which I similarly dump into the table of contents structure. Invariably I find by the time it comes to writing I already have substantially pieces of drafts and links to material which makes the hard work of actually turning out the finished product easier.
Frederiko