I've never been a good note taker. In the things I think about, when I'm really invested in something, I have to reverse engineer it to experience the why.

Reverse engineering can take several forms for me: it started with writing parts of systems from scratch, and now (due to academic training) it oftens looks like "thinking about how to explain the system to a group of colleagues", which is one degree of separation from writing the system from scratch, but is much faster - and seems to work well when working with LM agents on code (because you have to confront your ignorance)

part of the training in academia is how to know when you don't understood the thing, so this ends up working well for me now.

One trick: you can force yourself to understand something better by making a presentation and imagining you're going to be grilled by someone smarter than you. This is kind of the feeling of pressure that academic paper reviews give (in an ideal world) and it translates when you think about explaining something to someone else.