Zettelkasten along with writing a lot. Just write.

If you write code, you know the experience of just cranking out some shit and then refactoring a lot as you figure out how to phrase what you're trying to do. Writing prose is the same.

The bits that crystallize are small and reusable, so those are your atoms. Atoms bounce around and combine into larger lines of thought. Some go somewhere, some don't.

For taking notes on already synthesized material, I find it useful to rip through it as fast as possible the first time to establish anchors and important vocabulary. This is a good time to figure out if you have questions, determine if the material is actually useful or should be supplemented with something else, and roughly outline what information the material intends to transmit.

From there, you do a close read. Depending on the density of the material and how long you have, this can be as little as a page a day (even less for very dense texts). Don't try to understand how everything fits together, just extract things that seem important. Is there a term that comes up over and over? Is there a theme or technique that's referenced or applied in many places? Whenever possible, capture these in your own words with as much detail as you need to keep the idea self-contained. Do not copy from the text. Engage your brain. Synthesize information.

Now you have a soup of your own ideas, bootstrapped by the hard-won knowledge of somebody else but no longer bound up in the text. You are now free to connect these ideas, mix them in ways the text doesn't allow because it's just dead thoughts already packaged.

I'll underline the important thing again: just write! You get better at writing by writing, and useful note taking is just a particular form of writing. Don't worry about the audience, because the audience is you and your brain. If you need to package it for consumption before you've even begun, you'll hamstring your process. When you've built the bones of an idea for yourself, you can later turn those into an essay or what have you for others with all the extra context and references necessary.