Scrivener has a lot of nice features that allow a self-published author to create a nice looking ePub, which then can be uploaded to the iBooks and Kindle stores. Let’s call this the “direct” approach: Scrivener > ePub > Kindle.
I believe some writers export their manuscript from Scrivener, then use another tool for final formatting and aesthetic changes. They then submit this intermediate document to iBooks and Kindle. Let’s call this the “indirect” approach: Scrivener > Export > Intermediate Tool > Kindle.
I know that some writers use Microsoft Word or Vellum as their intermediate tool, but I’d like to know about other tools that writers use. If you use a different intermediate tool, please post the name of the tool and why you use it (what feature it provides for you that Scrivener itself does not provide). I’m just looking for ways to make ebooks look nicer and be more functional for the reader.
My current WIP was moved out of Scrivener for awhile for reasons, where I worked on it in Markdown format and occasionally converted it to ePub via Pandoc, a free command line tool for Win/Mac/Linux that can also output to Word, OpenOffice, LaTex, etc. From there I used Calibre to convert the ePub to Kindle. Things have moved back to Scrivener now.
I haven’t had the need yet to experiment with Scrivener to see whether its ePub output is as flexible as putting its MultiMarkdown output through Pandoc. Right now there’s something odd in my document structure that prevents Scrivener from breaking up the later chapters of my binder so they show up as chapters in my compiled Kindle ebook’s TOC, but it works perfectly when compiling to ePub. This isn’t a concern to me at the moment (I’m only compiling to ebook for my own convenience), so I haven’t tried to troubleshoot it.