reply to u/ethanzanemiller at https://www.reddit.com/r/Zettelkasten/comments/185xmuh/taking_notes_for_historical_writing/
Rather than spending time theorizing on the subject, particularly since you sound like you're neck-deep already, I would heartily recommend spending some time practicing it heavily within the area you're looking at. Through a bit of time and experience, more of your questions will become imminently clear, especially if you're a practicing historian.
A frequently missing piece to some of this puzzle for practicing academics is upping the level of how you read and having the ability to consult short pieces of books and articles rather than reading them "cover-to-cover" which is often unnecessary for one's work. Of particular help here, try Adler and Van Doren, and specifically their sections on analytical and syntopical reading.
- Adler, Mortimer J., and Charles Van Doren. How to Read a Book: The Classical Guide to Intelligent Reading. Revised and Updated ed. edition. 1940. Reprint, Touchstone, 2011.
In addition to the list of practicing historians I'd provided elsewhere on the topic, you might also appreciate sociologist Beatrice Webb's short appendix C in My Apprenticeship or her longer related text. She spends some time talking about handling dates and the database nature of querying collected facts and ideas to do research and to tell a story.
Also helpful might be Mill's article which became a chapter in one of his later books:
Perhaps u/danallosso may have something illuminating to add, or you can skim through his responses on the subject on Reddit or via his previous related writing: https://danallosso.substack.com/.
Enough historians and various other humanists have been practicing these broad methods for centuries to bear out their usefulness in researching and organizing their work. Read a bit, but truly: practice, practice, and more practice is going to be your best friend here.