I sometimes feel that the Zettelkasten-method doesn`t work that well if you really care about wanting to know everything about the source. It is just not possible to keep it atomic or focused on developing ideas as everything I read or stumble upon could theoretically be used for teaching. I therefore need to have some kind of structure note for the books so that I know in which book I can find something about a specific subject.
This is not true at all and reflects a misunderstanding of the ZK method. There is nothing in the modern, digital ZK method that says not to use a structure note – in fact the term structure note aka hub note is widely used in ZK circles.
What I recommend however is not focusing on chapters but rather focusing on ideas. Your notes build up a mental schema regarding how concepts fit together, and you can either build up a collection of chapters and then have to rummage through them to piece the ideas together, or you can focus on the ideas that wind through the chapters and make the ideas the organizing structure in your book note.
In my notes I create a single file for each source I process and take rough notes (text/images) directly in that source file. These are typically bullets that I jot down as I process the source. Those rough notes are often divided under chapter/section headings so they are tied to the sections where I read them. Then as I start to identify the same ideas showing up in different chapters I chunk those rough notes together so they are grouped together, with lots of whitespace between these chunks. As they flesh out I start to refine the chunks by rewriting pieces of them. Then when I feel a chunk is ready to become its own atomic note I give it a meaningful title by placing a single line above the chunk, usually in propositional-title form. Then I highlight the title + chunk and run the note refactor plugin. Now I have an atomic note, whose title is the first line of that chunk, and the note is linked to & from the source note.
Repeat until complete.
Doing this also allows me to link between the ideas as they are forming, since they often reference each other.
The point is to focus on the idea architecture not the chapter structure. Use the chapters as an initial structuring method but when you are done you should have an outline of mostly links in the source note.
You can look in my post history to see some examples of outline notes that I take. Longer sources typically look like that when I’m done processing them.