SQL uses a SQL instance name. That instance name could be the netbios name of the server or it can be a "named instance" that you configured. When you connect to SQL you connect to the instance name. The BES (regardless of it's name) will still be pointed to the "BESMgmt" database on the SQL server or it's "named instance".
The following thread..
http://www.blackberryforums.com/show...server+virtual
may provide some answers.....