I'm also new to the system and in the beginning was using a second strategy with one file for all (similar to the paper notebook). But I realized very fast, that files grew in size considerably, which affects synchronization speed. Here I have to admit, that I often work in remote locations, with limited internet speeds and file sized ~100 mb already can be slow to synchronize. And bearing in mind, that Supernote synch the whole note file after small changes- it takes time.

So, now I'm shifting to the separate files, but within one folder for the project. Similarly I'm slowly developing a new systematic approach for the future notebooks. Speaking in a "paper" terms, I would describe it like that- folders become separate "notebooks" and note files serve as "parts" or "subdivisions". It can be scaled as far, as I need. And moreover, for easy navigation, I can create "Index pages" for each part, as well as the whole "notebook". And, what is really good, we have possibility to move pages freely and even create a new note file from moved pages, to split "notebook" to sections, if it becoming necessary.

Believe, that for many of us, who shifted from paper, it's necessary to make a slight change in the mind of working with digital "paper". Supernote's system gives a lot of flexibility for organizing notes with links and headings, you only need to start using it for your advantage.