@wwydmanski
I read most of my articles digitally, and print out only the ones I have to study in detail.
I use #zotero, it allows you to associate notes to article.
For each article I make a note on zotero with all my notes about the article.
I read the articles from within zotero using the included pdf reader and highlight the article there.
Once I read a few articles, I write some notes to sum up the information; I do this using a different software for note taking.