Here are a few tips to remember when typing up your manuscript:

1. Use single spaces only, even at the end of a sentence. If you are an old-school typist, as I am, you were probably taught to use two spaces after a full-stop, but this is inadvisable on a computer. Some eBook converters will complain if they find two spaces together, and there is always the risk that one space will be put on the next line, forcing that line out of alignment with the rest.
2. Avoid using blank lines in your document. It is best to put a visual marker instead. If you really want blank lines in a finished printed manuscript, you can adjust them once the page sizes are known, but in eBooks you can never guarantee where the page breaks will fall, and it is very easy to miss a blank line at the top or bottom of a page. For this reason, ebook converters will complain if you upload a document with blank lines.
3. Indent the first line of each paragraph using the automatic settings in your word processing software. The usual style these days is to have no blank lines between paragraphs in fiction, and so the way to signal a new paragraph visually is to indent the first line a little. However, using the tab key or space bar to do this is a bad idea, as it makes it fiddly to adjust at a later date.
4. Use section breaks or page breaks at the end of the chapter, to push the next chapter to the top of a new page. Section breaks also give you the option to choose whether you want next page or odd page starts, and allow you to change the header and footer between sections.
5. Make use of the style system. Marking your headings using styles is not only a handy short-cut to keeping your formatting consistent, but it is the key to generating a Table of Contents for the front of the book, and if your book is non-fiction, then the navigation pane will help you check that your content is organised appropriately. 
6. Avoid using the space bar to align content on the page. Instead, use the left-align, right-align and centre buttons. For anything more complicated, you can always set and use the tabs, or use a table and hide the borders.

If you follow these simple rules when typing up your manuscript, the final formatting should be smooth and easy.

More information on using the style system and section breaks.