Is there a way to select what Note Notebooks show on the mobile app?
Not yet. It's currently all or nothing. We'd like to bring more granular control in the future, but we don't have a time frame for doing that at this point.
Thanks for your feedback. This helps us decide what work to prioritize.
For me I'd prefer either the old notes on mobile or a way to set highlights to go automatically into a notebook. At this point I'm in the middle and every highlight I make I have to go to the notes tool and manually add each highlight to it's resource specific notebook
I'm curious why you're doing this. Every note is automatically organized by the resource it was taken on. What are you try accomplish by putting them into a notebook? If you haven't read it yet, this article on the use of notebooks might help.