I do a lot of critical reading for school with my various devices.I have found the easy thing to do is have a notebook with me and just make notes in there.I make a separate section for each chapter/section and put a short annotation in the ebook and notebook to reference back to in each.
For example I will make a comment in my notebook about a paragraph and mark at the beginning something like b6 and put that as a note in the e-book to reference back to.
I have found taking long notes in electronic devices is to cumbersome for my taste.
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