Personally, I wouldn’t worry about the size of your documents so much. I’ve found it more fruitful to instead focus on:
- How can I best structure my ideas in RemNote, so that they reflect what’s going on in my head and so that they generate good flashcards?
- How can I organize ideas in RemNote to be able to quickly refer to them / find them / use them in the future?
RemNote thus includes a number of features that reduces the emphasis on document structures (portals, references to anything, etc.) so that you need to worry about this question less.
That said, I personally tend to have smaller documents, where each document comes from a single smaller source (ex. a single chapter of a book, single paper, single webpage, etc.) However, I tend to have large folders, with many documents inside them.
For example, if I start a new book I’d use a structure like this:
As @UMNiK points out, the Chapters can be documents that are either toggled open or closed.