After you've made revisions to the metadata in calibre (changed title/author/tags/cover), with the book highlighted in the main library window, click
Send to device.
If that doesn't work, select the book in the Reader window, click
Remove books, or delete the book in iBooks while disconnected, then reconnect and download it again from calibre.
There have been many bug fixes and code improvements in 0.7.3, scheduled for release this weekend. Simply sending the book again should do the right thing.
There is a
known caching bug in iBooks 1.0.1 that causes it to continue displaying the initial cover downloaded with a book. Unfortunately, the only way to get rid of the old cover is to uninstall iBooks. Hopefully that will be fixed in iBooks 1.1 which should be released 6/21.
G
EDIT: 0.7.3 is now available.