For my study of scientific-related subjects, I use GoodNotes and X-Mind.
As I am studying my math or statistics textbook, I would keep GoodNotes at hand. When I think I have accumulated enough concepts and steps while reading that is about to confuse me, I jog them down into GoodNotes in a self-explanatory layout, pictures, steps, tables, and so on. It helps me to dump them from my mind while creating space for more, and I also understand them by arranging the pieces and steps.
Then, actually not then, once in a while and sometimes at the beginning, I put the knowledge into a mindmap format with X-mind. It helps create a structure in my mind.
In X-mind, it’s a breakdown of knowledge structure.
In GoodNotes, you create notebooks, pages inside the notebooks, and page sections with the title.