I did most of the formatting and file uploading of Lyon's Legacy last week. Here are a few things I learned--the hard way.
1. No matter where you plan to upload your files, use the Smashwords Style Guide to get a nicely formatted version of your manuscript. It's free, and it walks you through the process. You can find it here.
2. Start using styles to format your manuscript, as they carry over through the conversion process. If you use the Smashwords Style Guide, it will talk you through how to create and modify a style.
3. Going along with #1 and #2, use styles to define your paragraphs. If you set up a style with an automatic indent, then you don't have to worry about tabs. (And apparently tabs are bad.)
4. Start using styles in your current WIPs, so you don't end up having to remove a lot of blank lines between paragraphs. It was bad enough doing this for a novella; it will take twice as long for a full-length novel.
5. When you publish through Smashwords, you will have the option to prepare e-books in various formats, including those for Kindle and Nook. Go ahead and include them, but opt out of distributing to Amazon and B&N. You can do this through the Distribution Channel Manager on your Dashboard. I didn't realize this was in a different place at first, so I panicked a little until I figured out how to do it.
6. Double-check all the information before you hit "Publish." For example, make sure you remove all references to Smashwords when you prepare the Kindle edition. (I wound up making separate files.) You can edit your information afterwards, but the process can take time. Amazon seems to take longer than PubIt! or Smashwords to accept changes.
7. Make sure the size of your cover file meets the requirements of the various sites. I had to use Paint to downsize the file for B&N and for MyIdentifiers.com.
8. If you want ISBN numbers for your e-books, you need separate ones for each format. In other words, your Kindle version will have a different number than your Nook file. Amazon and B&N assign their own numbers, but I think the ISBNs may be useful later on. If you publish through Smashwords, you need an ISBN to distribute to Apple and Sony.
9. Once you hit publish, the stories may be up sooner than you expect. Smashwords seemed to be the quickest, followed by B&N, with Amazon last. I published on B&N after uploading to Amazon, but it was available on B&N first.
10. Don't be intimidated by the process; just give yourself extra time to review formatting and what fields you have to fill out for each site. The sites do offer help as well.
I hope that was helpful. I'm no expert, but if anyone has any questions, I'll do my best to answer them.