Wheeew. That was more of a chore than usual.
Being a rather tech-savvy person (not to mention a pretty decent programmer), I haven't really had issues with eBook formatting before. Sure, it took a couple hours at the beginning of it all to learn the ropes, but after that I never had much trouble getting my books to look the way I wanted. Until yesterday.
So long as you upload a .doc file, Amazon's conversion process is a breeze. The only other version I tried was uploading .html, and that had some issues - mostly because the HTML output from both OpenOffice and LibreOffice is extremely flawed. I was about to dive in an fix it manually when I remembered I could just go with a .doc. I wish they'd just start supporting .odt, but oh well. Can't have it all.
Smashwords, on the other hand, is a different beast. A lot of people decry the Meatgrinder, but I've never had too bad of an experience. The only real beef I've got with the output is that their "Online Reading" view (accessible from the Smashwords store itself) butchers text stylings. It can't seem to take text alignment from the text styles, so all the centered text displays improperly. It makes the book look horrible right from the title page. Fortunately, not many people buy directly from Smashword's site, and the epub, mobi, and other formats all look fine. People who find my books on Apple, B&N, and the other stores will have a properly arranged product.
Still, it annoys me. I'll probably see what I can do about it later this year (maybe just start a conversation with the Smashwords people themselves and see if they can fix the way their Online View is put together).
The most... erm... amusing lesson of yesterday and today's formatting issues is that the epub validation process (required for distribution to Apple) can get a bit wonky. I don't know a vast amount about the process, but apparently it can mistake your style names for html tags and think that the file is malformed. I had a style called "blockquote" because it was for freaking block quotes and other text formatted like them; for instance, a missive from one king to another, printed verbatim on the page.
I ended up changing the style name to the more fanciful "LetterScribe." That fixed the problem. Still, it took unzipping the epub and going into the text with Notepad++ to find the source, and that was rather annoying.
Still and all, it's done. The book is published on Smashwords and being vetted on Amazon as we speak. Once Amazon comes through and tells me the thing is published for true, I'll be making the official announcement.