Dear Maiken Damsgaard Bøgh,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
We are sorry to hear that you’re having trouble customizing your staff notebook. I deeply understand the inconvenience this has caused and sincerely apologize for it.
Based on the description you provided; I understand your concern. Unfortunately, there is currently no out-of-the-box feature to customize the Class Notebook directly in the SharePoint Online site library, apart from creating the Class Notebook via Class Team in Microsoft Teams. It is not possible to apply customizations in the SharePoint library. Changing or editing content in the Staff Notebook folder may even result in errors.
The only other option that might be useful to you is using page templates which may be far from what you really want. You can be created or customized pages as described in the Microsoft Support article "Create or customize page templates - Microsoft Support" This can be applied if you are using the desktop version of OneNote 2016.
I agree that having the ability to create the Class Notebook directly in the SharePoint Online site would benefit users. I suggest you add your valuable idea as feedback in the SharePoint · Community (microsoft.com), which is the best place to share ideas and help improve Microsoft products.
Once again, I apologize for the inconvenience this has caused. We appreciate your patience and understanding and thank you for your time and cooperation.
Sincerely,
Ralph Chawatama | Microsoft Community Moderator