If you are using Word for your eBook, use styles. That's the best way to get as clean code from Word as possible. Do not highlight and then select everything you want done to that text. Select a style or if an appropriate style does not exist, create one.
Also, before you upload an ePub eBook, go through the code and remove any rubbish and clean up what can be cleaned up. You want to follow the rule of KISS. So keep your code as simple as possible. Do you know HTML/CSS?