To stop a named instance of SQL Server
net stop mssql$instancename
Note Stopping a named instance of Microsoft® SQL Server™ 2000 using SQL Server Enterprise Manager or the net stop mssql$instancename command causes SQL Server to perform a checkpoint in all databases. Then a SHUTDOWN WITH NOWAIT is done to flush all committed data from the data cache and to stop the server immediately. Stopping a named instance of SQL Server 2000 from the command prompt works only if you are running Microsoft Windows NT® 4.0 or Windows® 2000.