I wrapped a master's level class a few months ago, so my sample size is small.
I was able to buy my books as Kindle ebooks. From there, I used Apprentice Alf's tools to break the DRM on them and put them into iBooks. I would highlight the passages I wanted to cite and use the notes feature in the Kindle app. There is a place on the Amazon site you can download your highlights and notes.
I used OneNote for all my class notes. I had a separate notebook just for the class and used a different page for each week of the class.
PFDs, depending on what I needed I would usually use PDF Expert.
For citation management, I used EasyBib. I would use the export command "copy text" and paste it into the cited works section and format as needed.
Not sure if this answered your question.