I read a lot in a e-reader (Kobo) mostly books from the library (I get the epub files).
I have two ways of taking notes:
1) I use Standard Notes to register my own notes about what I'm reading. If it's a fiction book, I'll usually take note of characters names, places, interesting plot points, etc. I do that specially for books that I'm reading for my book club. I add my overall thoughts after I finished as well. These notes are not complex or long at all, I usually add them using my phone while I'm reading.
2) While I'm reading I highlight quotes/paragraphs that I find interesting in my Kobo and after I'm done I extract them the using a plugin in Calibre, and copy and paste it into the same notes file I created in point 1. This is specially true for non fiction books. Sometimes I don't even bother extracting quotes from fiction books.
I'm currently re-reading a non-fiction about writing that is quite interesting: Writing Down the Bones: Freeing the Writer Within by Natalie Goldberg
Great sci-fi series I'm enjoying: Planetfall Series by Emma Newman - 4 books set in the same universe that you can read in any order because each book is set in different places and timelines. It's sci-fi with touches of thriller, mystery, psychological themes, very engaging.
While I'm reading I highlight quotes/paragraphs that I find interesting in my Kobo and after I'm done I extract them the using a plugin in Calibre,
Had no idea this is a thing! I have a kobo but it stopped updating... But maybe I'll play around with this.
I will checkout planetfall, I think I'm in the mood for something like this.