It depends on the length of what I’m writing.
I’ll start off by saying that I used to always write entire chapters as one long document and leave it at that. In fact, I have done this since buying Scrivener in 2013 and only just stopped as of about a month ago. Why?
Because for the first time, what I was writing outgrew my ability to keep the total story in my head.
I was losing track of which chapters certain events happened in. For instance, one of my characters has had a few undiagnosed panic attacks. About 120,000 words into the story, I realized that I needed to refer to those scenes again. But how the hell was I going to find them? I had a vague recollection of where in the story they were, but 120,000 words is a lot to comb through to find a few specific scenes that don’t last very long.
I managed to find them by remembering how I’d described them and searching for the phrases. I keyworded those chapters (my first time seriously using keywords!) and went back to writing. A little later, I needed the scenes again, and searched the keywords. Then I realized another problem: the chapters themselves could reach up to 10,000 words each and that’s still a lot to comb through to find one scene.
And there were other events I needed to keyword, too, so that I could refer to them later or determine where they were in the timeline or how often they had happened. And keywording a whole chapter just wasn’t cutting it due to the amount of words involved. Finally I bit the bullet and spent a few hours splitting up all 120,000 words into specific scenes, naming them all to describe what they contained, and keywording each and every one of them. It has made keeping track of my story vastly easier and I wish I’d done it sooner.
That said, I still write new chapters as one long document. I have to. I can’t scene-split as I write, it interrupts the flow of my work and really throws me off. I just throw an asterisk between scene changes and keep going. But now when I’m done a chapter, I go back and split up the scenes into separate documents, tagging with keywords as I go. While this is frustrating when I need to re-read an entire chapter — I’m still getting used to viewing an entire folder’s subdocuments at once, because the line and large gap between scrivenings throws me off when reading — it’s far more manageable to search than one massive document. For this particular story, the trade-off is worth it.
However, for my shorter stories (under 60,000 words), I still write chapters as one long document, because there’s not nearly as many events to keep track of. As long as I can keep it all in my head, I’ll leave chapters as single files. My brain just likes that better for the flow of things, both writing and reading.