On several occasions I have written about how I use Devonthink Pro (DTP) for scholarly writing. Although at one point I had all my information on manuscripts in a single DTP database, over the last year I have maintained separate databases; one for PDFs, another for my annotations.
I accomplish this by having separate folders in Dropbox. After extracting my annotations from Highlights.app, I place the exported files in their own folder. Once a month, I export all the PDFs in my Paper’s Library to their own Dropbox folder. I use a Hazel script to throw away any duplicate PDFs in the Dropbox folder. I index (not import) the annotations folder into one DTP database, and index my PDFs into another.
This setup allows a fair amount of flexibility. Not only is this setup advantageous for writing with DTP (as I will cover in my next entry), it allows easy access to my PDFs for reading with Liquidtext or listening with Voice Dream.