So after a previous google search it would appear I've misunderstood metadata management all along...
This isn't quite like managing my mp3 collection.
Are opf files just metadata containers? What about the calibre .db file, isn't that a metadata container? Where are all the metadata updates I'm doing in calibre being saved to?
If I have a folder that contains an epup, an opf file, and jpg what is the correct method to instruct Calibre to import the metadata / cover image as well when adding the book?