I heavily use DT+BEAR. Here it goes:
- Files are indexed in DT. Sort-of PARA organization.
- The “second brain” (yeah right) is in BEAR. I have my 10.000+ notes there, with a lot of inter-linking wiki style and few tags, mainly context-based (ie work, teaching, etc.).
- If the note needs a link to a file, I paste the DT markdown link.
This setup works on all my devices, iphone, ipad, mac.