Choosing the schema that’s right for your Messaging Server installation depends on your provisioning needs:
Are you integrating Messaging Server with other Java Enterprise System component products, such as Portal Server or Access Manager, which provide single sign-on capabilities?
Are you installing Messaging Server for the first time or are you upgrading from an older version?
If you are installing Messaging Server for the first time, use Schema 2.
If you are upgrading from an older version of Messaging Server, you can either use Schema 1 or Schema 2.