The MySQL Server Instance Config Wizard is normally started as part of the installation process. You should only need to run the MySQL Server Instance Config Wizard again when you need to change the configuration parameters of your server.
If you chose not to open a port prior to installing MySQL on Windows Vista, you can choose to use the MySQL Server Instance Config Wizard after installation. However, you must open a port in the Windows Firewall. To do this see the instructions given in Section 1.3.1.1, “Downloading and Starting the MySQL Installation Wizard”. Rather than opening a port, you also have the option of adding MySQL as a program that bypasses the Windows Firewall. One or the other option is sufficient — you need not do both. Additionally, when running the MySQL Server Config Wizard on Windows Vista ensure that you are logged in as a user with administrative rights.

You can launch the MySQL Config Wizard by clicking the MySQL Server Instance Config Wizard entry in the MySQL section of the Windows Start menu.
        Alternatively, you can navigate to the bin
        directory of your MySQL installation and launch the
        MySQLInstanceConfig.exe file directly.
      
        The MySQL Server Instance Config Wizard places the
        my.ini file in the installation directory
        for the MySQL server. This helps associate configuration files
        with particular server instances.
      
        To ensure that the MySQL server knows where to look for the
        my.ini file, an argument similar to this is
        passed to the MySQL server as part of the service installation:
      
--defaults-file="C:\Program Files\MySQL\MySQL Server 5.1\my.ini"
        Here, C:\Program Files\MySQL\MySQL Server
        5.1 is replaced with the installation
        path to the MySQL Server. The
        --defaults-file option instructs
        the MySQL server to read the specified file for configuration
        options when it starts.
      
        Apart from making changes to the my.ini
        file by running the MySQL Server Instance Config Wizard again,
        you can modify it by opening it with a text editor and making
        any necessary changes. You can also modify the server
        configuration with the
        http://www.mysql.com/products/administrator/ utility. For more
        information about server configuration, see
        Server Command Options.
      
        MySQL clients and utilities such as the mysql
        and mysqldump command-line clients are not
        able to locate the my.ini file located in
        the server installation directory. To configure the client and
        utility applications, create a new my.ini
        file in the Windows installation directory (for example,
        C:\WINDOWS).
      
        Under Windows Server 2003, Windows Server 2000, Windows XP, and
        Windows Vista MySQL Server Instance Config Wizard will configure
        MySQL to work as a Windows service. To start and stop MySQL you
        use the Services application that is
        supplied as part of the Windows Administrator Tools.
      

