One fundamental organizational device I use is what is called a "smart topic" in ConnectedText. It may be thought of as the "reverse" of a wiki category, and it is just a topic with an embedded search. So, if I would like to have an easy way of knowing how many topics I have on the medieval university and its institutions, I could create a topic called "medieval university" and put the following inline query into it: "[[$ASK:medieval and university|Index|]]" and it will list every topic on the subject. (If you are curious, there are 24).
Over the years, I have found three types of smart topics particularly useful, one belongs to the category "Person," another to the category "Concept," and the final one to the category "Theory." So, if I want to know how many and what topics I have, say on A. J. Ayer, I just put "[[$ASK:Ayer|Index|]]" into my Ayer page. If I want to know how many and what topics I have on the concept of "order," I do the equivalent for it, and if I want to know about "string theory" the same. (I assure you that there are not many notes on the last topic [I checked and found exactly 2]).
Some people, including Luhmann, think that classifying one's notes by persons is a deficient way of achieving order. As a Systems theorist, he is somewhat disdainful of this approach:
One possibility is to remember names: Marx, Freud, Giddens, Bourdieu, etc. Obviously most knowledge can also be ordered by names, eventually also by names of theories such as social phenomenology, theory of reception in the literary disciplines, etc. Even introductions to sociology and basic texts are conceived in this way. What one cannot learn from such works, however, are conceptual connections and especially the nature of the problems that these texts try to solve. Still, even candidates in exams at the end of their studies want to be examined on Max Weber or, if that is too much, on Humberto Maturana, and they are prepared to report on what they know about these authors.Luhmann clearly thinks this is sub-par for the course. I don't disagree. That is why I also sort things according to concepts.
One might argue that this is still deficient. As Karl Popper claimed, "Theories may be true or false. Concepts can at best be adequate and at worst be misleading. Concepts are unimportant, in comparison with theories." And this is why I also have a category named "theory" under which I can find smart topics with searches for particular theories.
This is one way I organize my note-taking. It is by no means the only one, as I suggested at the very beginning.