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All styling information that you want to preserve in the ePub must be applied through the use of paragraph and character styles (and you should be doing this anyway, it's just good practice).
The book should have a ToC created within inDesign in order to generate the correct links.
The CS5 version of inDesign will automatically split the output into separate flows as long as your ToC is properly generated. If you're still using CS4, then you need to construct the book as a collection of documents (usually one per chapter), which will then be output as separate flows.
The more specific you can be about the problems you have, the more help people can give. Printing a book requires a certain amount of expertise, and the same is true of creating an ebook. It's not rocket science, but don't go looking for magical one-click solutions.
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