The UI for the IIS Manager seems to key off of the "Friendly Name" of the certificate.
For example if you have a wild card certificate that is installed for the server (i.e. *.mydomain.com) and you give it a friendly name of "wwwmydomain" then the UI protects the host header field when editing the bindings. To have the IIS Manager unprotect the HostHeader field, give the certificate a friendly name begining with an asterik "*" (i.e. *.mydomain.com).
With this friendly naming convention, the IIS Manager UI unprotects the host header field and allows you to specify your host header as desired once the certificate is selected.
If you already imported the certificate, you can use the Certificate Services MMC snap-in to change the friendly name of the certificate.
I'm uncertain as to why the IIS team doesn't specify this anywhere or if they know it can be done as I haven't found any documentation on this "feature", I just happened to stumble upon it while working in my development environment.
Hope that helps some of you out there in your day to day managment of IIS, however if you are doing any major management of IIS servers you should look at the Microsoft Managment APIs to automate much of your administration.
Cheers