I do things similarly to @Dpthomas87. (I’m in philosophy, but read a lot of old texts, medieval manuscripts etc., so lots of pre-processing there too.) I keep my references organized in BibDesk (which I can really, really recommend if you’re on the Mac), including my pdfs.
When I read and highlight a pdf article or book, I export the highlights to markdown, which goes into Obsidian. I name my lit notes by their citekey, and use tags pretty much the way Damon described it.
If I come across something that I think is very important, or just very well put, I tend to create a separate note for it (and link it to the main lit note). All these “snippets” get their yaml field with the author and the parent note, so that I can parse them later.
When I write, I have an “ideas” note as well, where I collect all kinds of things that come to mind about the project, as well as link to all the lit that may be relevant.
Nowadays I do my first draft writing in Obsidian and then export to latex for final editing and compiling.
Good luck with the PhD!