Note-taking for self-studying
There are two reasons (at least) for note taking   


creating a shorter, abstracted, version of your sources that you can save to return to later without recapitulating your whole education.   
learning something about the topic - getting it in to your head. 


For the former, you can type up notes as you go. Try to focus on the main points, not the detail. Leave lots of references in your notes so that you can easily return to the source as needed. 

However, if your objective is to actually learn the material from an operational perspective - using it - then typing up notes doesn't help nearly as much. Writing out things long hand is much better - but you may need to practice with the pen. And the fact that it is slow is also an advantage, since you engage with the material over a longer period. 

If you are studying for a field in which you want to become a professional, take notes by hand with a pen on good paper. In fifty years you will still be able to use those notes whereas the computer notes are likely inaccessible. 

The reason for long hand writing (even printing) is that your brain is more engaged in the process than it is with typing. That is how you learn - engaging the brain, not the motor muscles in your hands (unless you are learning a physical act like rock climbing or a martial art, where muscle memory is equally important. 

Moreover, to learn some subjects you need to also use the knowledge you are gaining. In math you solve a lot of problems. In CS you write a lot of programs. I History you pose a lot of theses. Whatever is appropriate, but it involves problem solving and creation in some way. 

See https://cseducators.stackexchange.com/a/1168/1293 for additional comments, including the other answers to the same question. 

If you search this site for "changing the brain" other hints will reveal themselves.