How do you "upload books to sites"?
When you change metadata for a book the changes are not written to the book format files in the library, however when a book is Sent to a Device or Saved to Disk the metadata in the file Sent/.Saved is updated with current metadata.
Use the Embed Metadata tool if you want to update the metadata in the library copy of the book; you may need to add it to a toolbar
To get a basic understanding of how calibre works, I suggest you watch the
Video Tutorials
BR