I have been using this a little bit. I just use preview and macOS to annotate the PDFs that I read, and they are stored inside of a data folder that org mode can use to attach to notes in an .org file. Right now beorg does not support attachments, which would be one feature that I would love to have. I keep everything in a GitHub repository.
This set up is far from perfect, but I have liked it more than trying to use Devon think or other tools, because I can still easily access all of the PDFs in the file system. I am really curious to learn about other workflows.