@greasemonkey, @anon27868835
Thanks for your replies.
I was caught between the same thoughts. I was taking small bitsized notes, but it was a hassle for me to then organize it again. Since, I was reading from a structured sources (maybe a few sources for same topics, but still more of less structured).
@greasemonkey, your suggestions are really apt for me as of now. I think I will stick to reading while marking (or commenting, as needed) and when I have the understanding of a chapter, I will come back here to create notes in more of a question/answer format (Some of them might end up synced with ANKI for SRS). This goes with what you suggested or I missed some point?
@anon27868835’s suggestion is welcome to me as well. I was trying something like this via zotero, but since I have kept all my books on GoogleDrive or Hard Copy, I feel better if I can just name it here and have a reference card of whatever I read. This would really help.
@anon27868835, should I keep marking the ‘indication’ whenever the content of the note changes pages (location in the book).
- I mean, I I have a topic on say page 23, and next is on page 25. Should I, in practice, include ‘indication’ before starting out note for the secon topic as well?
I agree with marking on the book or pdf as needed. It helps me to take me back to what I was thinking back then. 
Thank you for your suggestions 