For me, it helps to slow down my thoughts and aides deep work. I draw diagrams, connect blurbs with arrows, and “link” to other page numbers.
the "slowing down" part is the real value imo. i've noticed that the physical friction of writing (even just typing in a plain text file instead of a fancy tool) forces you to compress your thinking in a way that just staring at the problem doesn't.
there's a weird thing where the act of writing "i'm stuck because X" often makes the solution obvious before you finish the sentence. it's like rubber duck debugging but with yourself. i think that's what makes notebooks work for engineering specifically: the bottleneck usually isn't remembering what you did, it's noticing what you're actually thinking while you're doing it.
This is still missing the "what" for me. What do you write down about the work?
Is it a plan for what you're about to work on? Is it a breakdown? Is it facts you learn as you work through something? Is it a minute by minute journal of what you've done? Is it just interesting details? Is it to-dos? Is it opinions you're trying to clarify?
Diagrams I get, my desk is covered in scribbled diagrams to help me visualise something or communicate it to a colleague.