Until now, I’ve only really used a few features of Scrivener: the goal and wordcount feature, the folders, the ‘split at section’ command, and occasionally the research file.
This time I’m trying something different.
I wrote the whole of this draft in Microsoft Word. Because I wasn’t using any features aside from the wordcount and the putting-text-on-white-space features, it didn’t matter what software I used. Now I’m being a bit more discerning.
Sections
I opened a new folder on my project and pasted the entirety of my story into the first text document. From there, I went to the first scene break and split the story to the next section. 
By splitting the pre-written sections one at a time, I have the chance to really look at them without getting overwhelmed by how much I still have to do. I can thoughtfully evaluate when the scene actually starts and ends, figure out a title that won’t leave me hopelessly lost in a few days, and add a summary for my purposes.
Metadata
Scrivener has options for metadata. It defaults to descriptions of the chapter/section/idea/what have you, but I tinkered with it somewhat.
Because my story involves traveling between multiple locations, I set one to keep track of the country–this one by color.
I set the other one to keep track of the prevalent mood of each scene, both as the scene opens, and as it closes. I’ve mentioned before that we can’t just dwell on a single mood— it needs to continuously rise and fall to keep the readers invested.
Theme
I’ve been doing a lot of reading about theme in particular, and I’ve been trying to apply what I’ve learned so far. I’ve identified three core themes in my story, and the facets thereof that the different characters embody. Now that’s a lot of stuff. It’s too hard to keep track of all the themes of an entire story all at once. I’ve found it’s much easier to take it section by section and noting the themes that are touched on, and how they’re developed over the course of the story.
Characters
I’ve got a whole lot of named characters, so I use the Keywords feature to keep a track of which characters made an appearance in a given scene, and which ones were only mentioned. So far I’ve found that some of them are mentioned rarely enough to merit combining or cutting entirely (I’m looking at you, Kessie!), while one in particular needs a few more mentions to properly emphasize his place in the story.
Document Reference
There’s also a nifty feature that allows you to cross-reference the events going on in one section with stuff going on elsewhere. This becomes really useful for remembering exact details and wording of past conversations, keeping track of which saint deals with what aspects of life, and using the proper terms for all the parts of a dirigible.
The Cork Board
I’ve always admired the cork board feature on Scrivener, but I’ve never really had reason to use it before. Now that I’m taking advantage of all these other features, though, it’s a great way of seeing a lot of details at a glance.
What do you use to write and edit your stories? Are you big on features like these, or are you more a traditional ‘just-get-the-words-on-the-screen’ kind of writer?
JWTroemner.com 
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