I used and still use pen and paper, although for my discipline, I bought engineering paper so that I put graphs on the left page and content on the right page. That is what I used for lectures and presentations. There are limitations on a digital format unless you turn it into a glorified writing pad. You cannot mark arrows easily, you cannot easily link text to graphs and you cannot write marginalia as easily, unless you are typing in LaTeX.
Outside of lecture, I use highlighters. Although I keep a digital copy of articles, you cannot markup a pdf from a publisher. I maintain four inch binders that are organized in a manner that is useful for me. I have my own Dewey system. Electronically, I store the articles using tags as names such as serial_correlation_explosive_roots or mvue_cauchy_trimmed_mean. I also depend a lot upon memory. The difficulty of using a markup system is that you do not know what will be important in three years.
When you read an article it may be that keywords a, b, and c were what was important to you, but the article contained a seemingly uninteresting reference to keyword d, which is not a keyword because you don't care at this point in time. The keywords do not hurt, but if they cause you to commit less to memory because you say "I can search it," then you actually have lost retrievable data. Of course in an ideal world you would have built a search using the contents of the pdfs.
Pre-built bibliographic tools exist. BibTex is very useful, though not ideal. For continuity I use BibTex though if I were starting today, I may not. I maintain a unified bibliography for everything I have ever used or done. BibTex is part of LaTeX. If you are going to do professional writing, you should probably learn LaTeX. Download something like MikTex and then use something like TexStudio as a wrapper so you do not have to type out all of the commands. It isn't bad to learn on MikTex, but it is slower than TexStudio since TexStudio will guess what you are trying to do and autocomplete.