I have tried writing things I don’t want to forget, but I didn’t like it much. I have copied short quotes and added sticky notes at important parts, which I liked, but felt possibly not enough. I tried annotating, but it made me feel bad and disrespectful for the book.
I’m also in favour of going ham on annotating books because what use is a book if it goes unused?
The purpose of a book is to be read and to be used as a tool for learning, so use it as it’s been designed.
My caveat here would be for books which are first editions or extremely rare ones but that aside, use it as you will.
If you still don’t feel comfortable with that then you can use a pencil so that your annotations are erasable or you can buy sticky inserts that are transparent overlays which you can use to write onto which doesn’t cause any permanent impact on the book itself.
As for how you take notes, it depends on what your purpose is. I’m going to chew on this question and respond to it in another reply once I’ve mustered the brainpower.