I use confluence ( you can get a one person license for free) and completely outline everything I'm reading. Sometimes I use bullet points, sometimes I type in code samples using the code-block plugin. I use headers to divide chapters and sections.

I write everything - and if I can't understand it I type it in verbatim. Just the act of reproducing it often clarifies it in a way that reading ( or, if we're frank, skimming ) can't match. If I'm trying to understand Kubernetes CNI plugins

https://kubernetes.io/docs/concepts/extend-kubernetes/comput...

I'll type in exactly the statement

* Kubenet plugin: implements basic cbr0 using the bridge and host-local CNI plugins

And trust that as I go further in to the documentation I'll understand more and more what that means.

No copy-and-pasting. Type it in and force my brain to process it in and out. I've found it invaluable.