Whew. Copy-editing is changing how I think about formatting.
When I turn stories in to the Wordos or send them to a professional market, they need to look like they came off of a typewriter from 1988. In other words, a mono-spaced typeface, double-spaced, with inch-margins. Straight-quotes, two spaces after a period. Underlines for italics, and other "before the world had LaserWriters" formatting involving dashes. It's how I've formatted stories for the last ten years.
Formatting for eBooks is different. In traditional publishing, there's usually a type-setter working on an author's professionally formatted manuscript before it becomes the hard-copy a reader holds. So I need to un-learn some formatting habits if I am going to be producing an end-product.
For example, when I use Scrivener, I need to take advantage of its export functions instead of forcing formatting options at the raw document level. I say this because it's a real pain -- even with a wonderful tool like Scrivener -- to go through a document and curl quotes that used to be straight.
At least with eBooks I don't have to specify gutter widths and pantone colors.