One of the most productive people I know, took her lecture notes in the comment panel of PowerPoint in college, simply because _it's there_ when she open a lecture note. UI wise, it's probably worse than any note taking system that has ever showed up on HN. Nevertheless, she was a straight A student juggling 2 majors, 1 minor, and a lot of social life.
This is what I observed in hyper productive people: some of them have a unique, novel system of organizing their knowledge, but many of them don't. So, having such a system is probably not that important.
And even though I'm not a hyper productive person, this applies to what I'm good at doing as well. You can take away my favorite text editors/plugins/command line tools, and I can still competently write programs. I can code in notepad.exe if I have to. It won't be as convenient, but I can absolutely be productive.
It's the same for writing/reading/thinking. If you can already write, it's fine to try to perfect your workflow. If you can't write, it's not because you have the wrong pen.