Welcome!
This is a high-level overview of my workflow:
- Highlight relevant passages in PDF
- Review the highlights after completing the source document and copy those that stand out as particularly insightful into individual markdown notes
- Tag these “atomic notes” based on their topics and add a link back to the source document (incl. page) into a RTF custom metadata field
- Add cross-links between the atomic notes within the Markdown contents
- Transclude all insights with a specific tag for a topic-specific review
I would add that, from my perspective, it makes sense to actually go through these in stages. I find that when I’m looking at digesting a new input, it’s counterproductive to try to categorize each highlight then and there. There is actually more and deeper learning by doing one at a time (understanding, categorizing, reviewing, etc.), as there are different types of mental processes involved. My 2 cents anyways 
Good luck setting up your workflow - DT is incredibly flexible and adaptable, you’ll surely find one that works for you.