I've been spending some time studying several different subjects so I'll try to describe my approach. This is mostly just a hobby for me so I don't have any real criteria for evaluating how well it works but so far I feel reasonably satisfied with it.
For every subject I create a subdirectory for downloaded resources and an emacs org mode file for my notes. Unlike you I much prefer typing notes to handwriting. For math you can use latex and display previews inline in your org buffer. The only disadvantage is for drawings. I don't currently have a good way to capture those.
Generally my first step with a new subject is to try to find good online resources for it. That usually ends up being a collection of websites, PDF files that I download and YouTube videos. I often include links to websites and videos in my org file.
Next I try to get an overview of the subject and what particular topics I think I'll need to get an understanding of to reach my goals. I typically create sections or subsections in the org file for those areas.
When watching or reading content questions usually come up about things I don't fully understand. I try to write those down in the org file and at some point find information that helps to answer those questions, which of course I also note.
I don't try to take lots of notes or copy everything in the resources I read. I'll just note points that seem interesting, surprising, important, difficult and/or easily forgotten.
I'm not sure any of this will help you but that's my basic methodology.
One other thing you might want to look into are spaced repetition apps like Anki. I haven't personally made much use of them yet but I think they should help with subjects where there's a lot of material that needs to be memorized.