In the zarafa settings you select the domain. Usually the main Zentyal domain.
Then in the user settings which will default to the main zentyal domain. You can select the mail domain and if this is a zarafa member & quota.
The user must be of the same domain as zarafa is set to. Also you just put %username% and password to logon.
Roundcube can logon onto virtual domains and that is why when you logon you %username% & FQDN
So say we had a domain called zentyal.com and it is the main domain.
the zarafa login would be username / password
roundcube virtual domain would be
username@zentyal.com / password