Once you have downloaded and installed iPhone Configuration tool you have to create a configuration profile under LIBRARY.
Enter Wireless details under general (once you have selected new to create a new profile). Under the Credentials tab, click 'Configure'. An 'Add Credential'. The certificate should be listed if you have installed the certificate on your own machine if not you can add them by accessing mmc (start-> run -> mmc or start -> type mmc in search). Once in mmc you have to go to file, add/remove snapin and add certificates. Once you have done this you can now specify under the wifi, configuration tab the type of authentication to use.
Then under devices you can install it to the iPod/iPhone and setup the wifi configuration under settings, wifi.
If you have trouble adding in the certificate into the iPhone configuration tool such as what is shown below the solution is to tick allow export when importing the certificate into mmc.
Error Message: Certificate Exception: InitializeWithCertificate: Unable to export certificate due to exception: Key not valid for use in spcified state.