I don’t think that sorting or categorizing is necessary at all. Your notes have to be ideosyncratic to be useful anyway, being full of interpretation and your ideas and the like. Why use a system that anybody else can make sense of, then? You’re not the Library of Congress after all.
So when it’s becoming important to make sense of stuff and be creative, which means: connect things and generate new notes, then you’d be fine with a system lacking any hierarchy at all. Links between notes and shared keywords/tags will create clusters over time, though. This way, your system will create topic clusters by itself and generate internal hierarchies you wouldn’t have imagined before. This is the foundation of card index-based information management from centuries past. In German, this is the foundation of a “Zettelkasten.”
Like David Allen said in [i]Getting Things Done[/]: bottom-up planning is more useful in your daily work. Top-down planning like deducing from principles and pondering hierarchies seems to be sound advice at first. In the end, though, going with the flow and focusing on the process will yield more manageable results. Hierarchies emerge, you needn’t impose them.