In configuration manager, under the SQL Server 2005 services you should have a service for instance of SQL
SQL Server (MSSQLSERVER) -- Default
SQL Server (Name of Instance1) -- Named insatnce 1
SQL Server (Name of Instance2) -- Named instance 2
You will need to hit stop three times to stop all the instances or stop once for a particular instance.
Gethyn Elliswww.gethynellis.com