Welcome to the forum.
There are probably almost as many ways of producing ebooks as there are readers of this forum, and some of the advice and opinions expressed here have both proponents and opponents - including what I've just written.
My opinion, for what it is worth, is
- It is best to start with a Word document
- The Word document should then be marked up to valid XHTML
- And then packaged up to valid ePub format for Sony, Kobo, Nook, and iPads
- Then the valid ePub can be converted to mobi or azw3/KF8 for Kindles
- I suggest that you take pains to remember that ebooks are not print books.
I've obviously grossly over simplified the process - there are many different on ways of achieving the main steps in the list above - but it's a start for discussion.
I think most people would agree that pdf is the world's worst document for conversion into ebooks, and most people would agree that ePub and mobi or azw3/KF8 are by far the most important output formats.