I stumbled across this article by Richard Carter that describes how Charles Darin took notes.

If you were to keep a portfolio open for a couple of years, and throw in slips of paper as subjects crossed your mind, you would soon have a skeleton (and that seems to me the difficulty) on which to put the flesh and colours in your inimitable manner.

Darwin would mark up books, write literature notes, and even create a rough abstract of the books he read. He originally would use bound notebooks but later found them too restrictive, favoring the loose slips of paper instead.

The main takeaway is that he did not create a perfect system from the beginning, It always changed. The key is to capture notes and revisit them to create something useful.