The kindle only need the MOBI file. The other files wont bother the kindle they just take up space.
In calibre at the side of the "save to disc" button is a dropdown selector, the last option at the bottom is "save single format to disc" this will ask you which format you want to save, that way it can just save the MOBI format etc... without the need for a epub.
In calibre at the side of the "save to disc" button is a dropdown selector, the last option at the bottom is "save single format to disc" this will ask you which format you want to save, that way it can just save the MOBI format etc... without the need for a epub.