Tools for thought are tools for orientation. They’re the big circle in the OODA (observe-orient-decide-act) diagram. A tool for thought…

• Expands your awareness. The more you sense, the broader your ability to orient in your environment.

• Builds up a memory across time. Expanding your time horizon into a long now lets you act across broader timescales, lets you generalize across wider distributions, and avoid fat tailed risks.

• Broadens the surface area for luck to strike, by collecting stepping stones that expand your adjacent possible.

• Increases your bandwidth for synthesis by augmenting our intellect, and provoking creative insights.

• Evolves the complexity of your world-model. The bigger the memes, the complex-er your thoughts.

Knowledge production is a group-activity, not an individual one. Computers most radically and usefully extend our capabilities when they extend our ability to collaborate to solve problems beyond the compass of any single human mind. (Doug Engelbart)

I recently learned Einstein used to do something specific. To get his brain in the zone, he would bring together two very different things to see what the connection was between them. Are.na at its best is really good for that. So if I haven’t used Are.na in a more concentrated way in a while, I’ll just make a channel. Sometimes it doesn’t work out, but I’ll make a channel that’s very fuzzy. I’ll start to put stuff in it and just see where it goes.

Four principles
Writing is the only thing that matters.

Don't just read. Make reading notes. Don't just learn. Make blog posts or something to share what you learned.

Also, hand-written notes has some advantage. In (Mueller & Oppenheimer, The Pen Is Mightier Than the Keyboard: Advantages of Longhand Over Laptop Note Taking, 2014), it's shown that students who take notes by laptop understood lectures less, due to their tendency to transcribe verbatim without understanding. From mouth to ears to fingers, bypassing the brains completely.

The way I see it, this is not an argument against using the computer, but an argument for repharsing instead of copy-pasting/direct quoting/mere transcribing.
Be simple

Don't underline, highlight, write in the margins, or use several complicated systems for annotation. It'd make it really hard for you to retrieve these scattered ideas later. You would be forced to remember with your biological brain to keep track of what information is put...