You should strive to structure your notes based on the concept they represent rather then by their source (book/article) or project.
It's easy to start taking notes based on the book you're reading, but such notes have very limited long-term value. When you read a new book on a related topic - if you follow this approach you'd end up with two separate set of notes that are hard to relate to each other and combine.
When, on the other hand, you write your notes based on the concepts they represent - you'd be able to accumulate the insight on the topic over time. Improving and developing you thinking as you add to the note.
It's not just about adding new information to the note, but also about seeing how the new information integrates with your previous thinking - do they agree or contrast? Figuring out how to synthesize your previous thinking and new insight would allow you to develop a deeper understanding of the topic.
You'd be repeatedly coming back to the same concept note, as prompted by a new book or an article you read. And as a consequence it'd make easier for you to discover connections between these different sources of knowledge.
It's more challenging to create a proper new concept note if you compare it to creating book-based notes. It requires you to come up with a good way to represent the new concept as a standalone entity and to link it to related concepts. But it's actually a good thing, as it makes such a note more useful - To properly grok new information you need to actively engage with it
This synergizes well with the idea that [[evergreen notes should be atomic]] - highlighting that each concept should get it's own note.