As part of our automated build procedure we are trashing and reconstructing our IIS site with powershell scripts.
Once i have created the AppPool and the website com
I've found an example here on how one can assign the certificate.
http://learn.iis.net/page.aspx/491/powershell-snap-in-configuring-ssl-with-the-iis-powershell-snap-in/
However, it doesn't seem very elegant having to hard code the certificate thumbprint ... so if any one knows of a better method, I'd be glad to hear.