Metadata separate entry Help

Need some help please.

When I add a ebook that has a metadata opf file Calibre adds the ebook and the metadata as 2 separate entries

1. the ebook with name and author
2 no ebook but name and author with all the tags and info.

I can merge them but I don't want to add a lot of book and have to merge 100's of files.

How can I set it up that they get added as one entry?

Thanks