[DiapDealer]

calibre's metadata.opf file is simply what it uses for metadata storage in its own internal database. It has no bearing on the "real" metadata stored within the epub (until you save or send as doitsu indicated above). An epub will only make use of one opf file. There is no reason to try and add calibre's external opf file to an existing epub's archive.

If you don't want to add the meta tags by manually editing the opf file in Sigil, as Doitsu said above... you need to use the "Save to disk" feature of calibre. That will cause the custom metadata in calibre's metadata.opf file to be written to the resulting epub's internal opf file. Or you can do an epub to epub conversion within calibre. Or you can use the Modify Epub calibre plugin to update the internal metadata. I'd highly recommend the last option. It doesn't require creating an extra copy of the file and doesn't mess with any existing html/css.