If you have uploaded a book and then been disappointed when you have checked it on your Kindle (or had feedback from readers criticising your format) this may be a solution:
For those of you who asked, this is what I noted.
I have a Macbook Pro (2009) and initially used Microsoft Word to write my books. I thought that saving as a PDF would do it for a Kindle upload, but no, the formatting went out the window but looked OK in the preview. So, what I did was go to my bookshelf, choose the book for reformatting and choose edit from the actions menu. Previously, I had re-saved my beautifully formatted file as an html file. Then I re-uploaded it. This kept the format (with hard page breaks and indents).
Hope this helps you!