If you're just needing to set that domain as default so users don't have to type in the complete 'email@example.com' to login they can just type 'user':
Did you previously have a Split Domain - Zimbra :: Wiki setup?
zmprov mcf zimbraDefaultDomain domain.com
If so primary or secondary?
Like if primary you change the zimbraMailTransport.
If secondary you remove the zimbraMailCatchAllAddress & zimbraMailCatchAllForwardingAddress, any zimbraMtaRelayHost and turn back on zimbraMtaDnsLookupsEnabled
Assuming your just interested in changing firstname.lastname@example.org to email@example.com
Admin console gui > domains > make a new domain if you haven't already.
For a moment leave the old domain intact.
zmprov cd domain.com zimbraAuthMech zimbra
Also leave the admin, spam, ham, and the wiki account untouched right now.
To move any accounts you've already created over:
In the admin console gui you can just change the drop down box in the individual account > general tab to the other domain (just to the right of where you assign a username).
zmprov equilavent would be ra (renameAccount)
See this article if you need to script for a large number of users Bulk Provisioning - Zimbra :: Wiki
After you get done you should run a full backup-too lengthy to explain why here.
Note: As of 5.0beta2/3 there's a command to rename the entire domain:
zmprov -l renameDomain (or 'rd' for short) domain.com newDomain.com