You'll have to elaborate on which scenario you fit:
a) Leave the existing domain alone for a sec & create a new domain (use the admin console gui or it's like zmprov cd mktng.domain.com zimbraAuthMech zimbra)
Then: zmprov mcf zimbraDefaultDomainName desired.default.domain.com
(As for the unused domain, you can either leave it or delete it after you're sure you have all the admin/notification email attributes moved/changed.)
b) If your on v5B3 or greater there's the command zmprov -l renameDomain {domain|id} {newDomain}
c) If you need to change your server's hostname be sure to make a backup and follow
ZmSetServerName - Zimbra :: Wiki