Shawn’s admonition to keep things simple is valuable. I’m hoping to go through his excellent looking class materials shortly.
I rely heavily on Hypothes.is for digital annotation and transport it all into Obsidian using https://boffosocko.com/2021/07/08/hypothes-is-obsidian-hypothesidian-for-easier-note-taking-and-formatting/
@natalie recently wrote up an excellent overview for dovetailing with Zotero, which I’d done previously and love: https://nataliekraneiss.com/your-academic-reading-list-in-obsidian/
If you really want to go down the rabbit hole: https://boffosocko.com/research/zettelkasten-commonplace-books-and-note-taking-collection/
If it provides some reassurance, though I’ve not gotten into the specifics I’m reasonably certain that Marcel Mauss and Claude Lévi-Strauss, among many others, had significant practices.
If you’ve not found it yet, Obsidian has a Discord with a specific channel for academia.