To upgrade Ignite, run the windows installer and choose the same location to install the new software over the older version. The install process should handle the entire upgrade automatically. If it fails, make sure the "Ignite PI Server" service is shutdown and try again.
If you want to install the new version in another location, stop the "Ignite PI Server", install the new version in a different directory, and then copy the ignite_config directory from the old installation to the new installation. The ignite_config directory is located in <Ignite Dir>\iwc\tomcat.
Also, please note, if installing Ignite on Windows 7 or Vista, you will need to right-click on the 'setup.exe' and 'run as administrator'.