Wish I knew how to help, but I know zero about Scrivener. All you people and your fancy word processors, I swear.

I still use good ol' 2007 Microsoft Works - yup, not even Office, I use Works - for my story in a single document, formatted to make export to ebook formatting easy to do, and if there's any notes I need to keep track of, I use Word Pad docs. I find other word processors to be too cluttered or, worse, too organized. I just can't stand the way things like yWrite and Scrivener are set up for some reason. Atlantis Word Processor is alright, but it's basically Works+ and I still ultimately prefer Works.
I've considered
maybe putting some information into LitLift, not that it's really a Word Processor, when I reread my story to begin the second draft a couple weeks/months after my first draft is finished, so I know what needs to be fixed/what happens when I change something. But that's the most fancy I plan on getting with technology for writing this novel.
Unless you count scraping together some sc-ifi stock photos to make cover art for an e-book version, anyway.