I did not make separate notes.
However, I did digitise all textbooks I read and underline all relevant portions. I also used to add sidenotes wherever relevant.
I would also makes funny doodles ( Some of them downright offensive. However, the trick to memory is to make them really offensive. Our mind catches on such things and never forgets) on the side with my digital open.
Here are some samples.
Digitised Bipan Chandra
Digitised Geography ncert.