In the editor, assuming the cover image is in the 'Images' list, use
Tools->Add a cover, and select the image. Then you should see a
titlepage.xhtml file with the cover in it. Then you'll probably want to delete the 'other' one.
The
EpubSplit is an easy way to split omnibus editions, but I don't know if it will deal with the individual covers for the 'sub-books'.
BR