The MySQL Server Instance Configuration Wizard is normally started as part of the installation process. You should only need to run the MySQL Server Instance Configuration 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 or newer, you can choose to use the MySQL Server Configuration Wizard after installation. However, you must open a port in the Windows Firewall. To do this see the instructions given in Section 2.3.5.1.1, “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 Configuration Wizard on Windows Vista or newer, ensure that you are logged in as a user with administrative rights.

You can launch the MySQL Configuration Wizard by clicking the entry in the section of the Windows menu.
Alternatively, you can navigate to the bin
directory of your MySQL installation and launch the
MySQLInstanceConfig.exe file directly.
The MySQL Server Instance Configuration 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 5.5\my.ini"
Here, C:\Program Files\MySQL\MySQL Server
5.5 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 Configuration 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
Section 5.1.4, “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 Configuration 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.