Наконец-то я получил решение. Это код, который я хотел.
ServerManager serverManager = new ServerManager();
Site mySite = serverManager.Sites.Add(siteName.ToString(), "http", "*:80:" + domainName, physicalPath);
X509Store store = new X509Store(StoreName.My, StoreLocation.LocalMachine);
store.Open(OpenFlags.OpenExistingOnly | OpenFlags.ReadWrite);
X509Certificate2 certificate = new X509Certificate2("SSL server certificate", "password", X509KeyStorageFlags.Exportable);
store.Add(certificate);
var binding = mySite.Bindings.Add("*:443:" + domainName, certificate.GetCertHash(), "My");
binding.Protocol = "https";
mySite.ApplicationDefaults.ApplicationPoolName = siteName;
serverManager.CommitChanges();
store.Close();