bliff
The organization process is wholly dependent on how much I come up with in a day/week. I mostly read for fun now, so I don't have to rigorously organize lecture notes or anything like that for later use. On the other hand I'm pretty rigorous with how I process tasks. As a ballpark figure I'd say 30-60 minutes per week, or 5-10 minutes per night.
To your latter point, I think that's fair. The main idea is to be flexible and recognize when you need new categories or whatever (and when you can dump unhelpful ones).
I then have derived categories from the main stream of thoughts. If the thought is a task, I further process these into categories. I have recurring tasks and events that I handle on a "Time" page that is effectively a calendar, and I have one-off tasks that go into a Kanban style backlog.
What I really got from Zettlekasten is that trying to establish your system upfront is a mistake. Things inevitably leak through your categories and then you lose faith in your system. By just having a running stream of thoughts and then relating them after the fact and deriving categories afterward, you get the benefits of organization without a lot of its failure modes.