I think you meant to reply to @laudunum’s post aobve.
…freaking magical.
The way to do it is not to import your PDFs: leave them wherever Zotero or Bookends places them – Bookends just keeps them in a single directory in the iCloud Drive directory (because I sync with an iOS device) and index them in Devonthink. Then annotate them in PDF and DT creates a new folder called Annotations which, if you have added the links that DT lets you create, will take you straight to the spot in the PDF that is referenced in the annotation.
…but I can give it a try.
Pick your reference manager, Bookends or Zotero. I use Zotero. Add your references to the ref manager with the PDFs attached:
Now, in DEVONthink, add the folder where your reference manager stores PDFs (~/Zotero/storage) as an indexed folder:
Now, annotate the PDF using the application of your choice (I use either Preview or DT–and sometimes I open them from DT and sometimes from Zotero–it doesn’t matter) and DEVONthink will display those annotations and allow you to jump right to that annotation:
There may be other steps that others use, but hopefully that helps a little.
EDIT: spelling errors