See the Polish Books tool (if it is not in your toolbar, you can add it from Preferences ==:> Toolbars).
Polish Books can perform a number of changes, including subsetting fonts, embedding updated metadata/covers into the EPUB/AZW3 internal metadata fields... and of course, creating a Book Jacket and inserting it as a "page" in the front of the ebook.
It is also capable of recognizing existing Book Jackets and updating them rather than inserting additional ones.
