You've probably seen an e-book with horrible formatting -- half-lines, gaps where there shouldn't be any, phrases left out, disappearing images, blanks. And you know how annoying they can be. I know of no quicker way to drive your readers away. You must either resolve to learn the rules or to pay someone to do the formatting for you. But under no circumstances should you let your traditional publisher do the formatting for you. Not only do most not understand the rules -- they also have no stake in producing an e-book that readers can buy more cheaply than their own print version. I usually have CreateSpace do my conversions for $65.00 a book, because they are a branch of Amazon and understand the process.
A Kindle or other e-reader is NOT a book. Its size is not set; the reader can make type larger or smaller. It has no pages, and you can't open it at random. You can't easily read the last page first, if you're one of those who wants to know what happens in advance. Its multiple files are a mystery to most of us who are used to typing manuscripts in linear fashion. Fortunately, however, there are rules to help you produce a working Kindle document, even if you don't understand a thing you are doing!
Once again, let me remind you to consult the full set of rules in the free Kindle publishing guide, which you can download at: <http://www.amazon.com/dp/B00822K3Z0>. And be sure you download a fresh copy just before you are ready to begin the formatting, in case Amazon changes the rules. (They tend to do that!)
Start by taking your .doc file and doing a massive "search and replace" operation on it. Remove all hyphens within a word, all tabs, all double spaces, and all double paragraph breaks. Get rid of all headers and footers, including page numbers (Kindles don't have pages, remember.)
Do any necessary formatting by using the "Format Paragraph" menu. You can choose the size of your paragraph indents there, but keep them small. You can also choose to leave a space between paragraphs if you prefer not to indent. Just don't do both.
Before you submit your file, be sure to preview the document on the KDP publishing website, just to be certain that it looks the way you want it to.