I thought a lot about this and tried several different methods in my early twenties. I encourage you to abandon this pursuit and let your human mind perform it’s most wonderful magic: synthesizing, compressing and expanding mental inputs. Don’t get in the way of this magic: throw everything you can into the input chute and marvel at the connections that result.
Namely: Things like mindmaps and lots of little individual connected nodes (e.g. Obsidian) appeal in theory to human minds, because that's how our minds work.
But for me, I realized they weren't good tools for this because my brain is much much better at doing this than the software.
Ah, yes then: The software is good at 1) writing things down verbatim for detail and 2) re-reminding me of them when I go to look at them. The other stuff, the thinking and the connections, that's ME. That's NOT the software.
So for me that means. What I look at on the computer needs to be dense and well organized, not a mess of nodes. Which usually leads back to bigger, simpler chunks. I still use http://zim-wiki.org, but try to minimize the number of pages.
(To go broader, yes, this has very much deepened my skepticism of AI and machine-sentience)