You can use Microsoft.Web.Administration namespace to create a binding and set the certificate hash. Let us say you are trying to add a new binding to a website “MySite” with a new SSL certificate hash “MyCertHash”, here is what you have to do to achieve this
ServerManager serverManager = new ServerManager();
serverManager.Sites["MySite"].Bindings.Add("*.443:", MyCertHash, "MyCert");
The bindings member configures [...]