How to process your reading
You should start by reading the text, highlighting, and writing in the marginalia. If you get distracted, pull yourself back to the text. Don’t make atomic notes during this time — you want to focus on gaining an understanding of the main points of the text, and highlighting key points that add evidence to those main points along the way.
If you find additional reading that seems relevant, decide how long that will take you to read through. If it’s a big diversion from what you’re currently working on, add it to a reference manager or read-it-later app. If it’s a few short paragraphs, read through them and process as normal. The major issue with read-it-later apps is that you lose momentum when you come back to those things later, or you forgot why you wanted to read it. Don’t just tag the new article — take a note on it that tells you why you wanted to read it in the first place, and what ideas it relates to.
Once you’re done reading the text, you’re done with it. If it’s a scientific paper (Reading Scientific Papers), extract the highlights using Zotero and start skimming through the highlights. Cluster them according to their underlying broader concepts. It can help to lay out all the highlights and fleeting notes onto a canvas or mindmap. Then, take atomic notes on those (Notes should be atomic and disparate). See: Development of thought
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