You must find the port number on which the Backup Exec SQL 2005 or 2008 instance for the central administration server is running, and then create an alias for the managed media server.
To create an alias when a SQL 2005 or 2008 instance is used
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On the managed media server, to create an alias for the managed media server, go to \Windows\System32 and double-click cliconfg.exe.
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In the Server alias field, type:
server name\instance name
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In the Server name field, type:
server name\instance name
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In the Port number field, type the port number of the remote Backup Exec SQL Server instance.