So the Microsoft.Web.Administration API is very easy to use to create HTTP and HTTPS bindings for sites:
using (ServerManager manager = new
There is a method overload for adding Bindings that will add the certificate to HTTP.sys correctly, see: http://msdn.microsoft.com/en-us/library/bb355650(v=VS.90).aspx
Optionally you can actually set the binding settings:
binding.CertificateHash and binding.CertificateStoreName and when commiting it will register correctly with HTTP.sys: http://msdn.microsoft.com/en-us/library/microsoft.web.administration.binding_properties(v=VS.90).aspx