I am still honing my methods, but I figured I would write a little bit about what has been working for me. Before I start reading/note taking, I enter everything into Zotero, including tags. I used to include notes here, but I have found I prefer One Note for that. I don’t have an image here, but for PDF reading I have been using Devinthink which is great for organizing/annotating PDFs though it’s a pretty powerful program.
I first take notes in my notebook (a leuchtturm1917) because it’s easy for me as I am reading to just write things down. Here, I write down important points, quotes, keywords, etc. I then type these up in One Note, where I store them as show below.
I also try to write a two paragraph summary about the argument to really make sure I understand the stakes of the text and can integrate all of the points I found important enough to note.
With literature, rather than monographs, my approach is a bit different. I mark quotes and note taking inside the book and then transfer all of that to One Note after I finish. With literature I also make a bit more use of the tagging features.
So, overall I am using a leuchtturm1917, One Note (which I switched to from Evernote but either would be fine), Devinthink for pdfs and annotation, and Zotero for my bibliographic data. It is a lot of stuff, but most of it is free and so far it is keeping me VERY organized.