Having just made it through the process of getting Savage Fire published, I thought I would share what I learned while formatting, first for Amazon and then for Smashwords.
Lesson 1) Format for Smashwords first, and then for Amazon. The Smashwords formatting guide is good, if extremely demanding, but it helps you lay things out right from the beginning.
Lesson 2) Read and follow Guido Henkel's excellent series, Take pride in your eBook formatting as you prepare for the Amazon publishing. Since the early stages of Guido's process suggest using Word, start with the Smashwords, get it working, save a copy and then start with Guido's steps.
Lesson 3) Calibre is awesome (and free) software, but don't use the PDF they create unless you want to use it on very small devices. It sizes things as if you were using an iPhone. The Smashwords PDF is far better, but you can also use a product such as PDF995 to print from the Smashwords document to PDF. If you plan to do that, insert the cover image into the first page before you create the PDF.
Lesson 4) Don't start formatting until you have absolutely finalized the editing. Making changes in the prepared document can be done, but it is where most errors come in.
Lesson 5) Add two hard returns (hit enter twice) before you insert a page break and set the style for your chapter heading. Otherwise, the font and style mess up the last paragraph on the page before.
Lesson 6) Check and double check your final, formatted document in every format you can.
Lesson 7) Since both Amazon and Smashwords allow sampling, test the samples to make sure they don't end in an obnoxious way. I don't know how easy that is to change on Amazon, but on Smashwords it is very easy to change the percentage. I wish they allowed you to set a mark as the "end of sample", but I couldn't find one.