For PDFs, I agree that Microsoft Office is a great way to go if you have it: the results are excellent. If you don't,
LibreOffice is a free office suite, or a you can use a program like
Tomahawk PDF+.
For eBook files, I use
Calibre to manage and convert them. I can e.g. edit a book in Word, export it to HTML, tidy it up a little if I think it's needed, then import it to the Calibre library. In Calibre I can add the "metadata" such as title. author, cover art etc., then convert it to the required eBook format. (I only use ePub, but Mobi files for Kindle are created the same way.)
PDF and eBook formats are designed to do different things and should not be confused. PDFs are designed to look like the printed page, and so the text and graphics are in fixed pages. eBook formats like ePub and Mobi are more flexible, and are not forced to look a particular way. For example, changing a font size doesn't break the formatting, and page breaks are for the device or application to put in if needed.