I am using the following code to programatically create a web application & sub site,

            try
            {

                SPWebApplicationBuilder webAppBuilder = new SPWebApplicationBuilder(SPFarm.Local);

                SPWebApplication newApplication;
                int myPort = 3333;
                webAppBuilder.Port = myPort; //Port No.
                webAppBuilder.RootDirectory = new System.IO.DirectoryInfo("C:\\Inetpub\\wwwroot\\wss\\VirtualDirectories\\" + myPort);
                webAppBuilder.CreateNewDatabase = true; // Create new database

                webAppBuilder.DatabaseName = "WSS_Content_372772890a5a4a04abb460cd9ea3bd22";    // Database name
                webAppBuilder.DatabaseServer = webAppBuilder.DefaultZoneUri.Host;  // DatabaseServer Host name/computer name          

                webAppBuilder.UseNTLMExclusively = true;  // Use NTLM authentication

                newApplication = webAppBuilder.Create(); // Create new web application
                newApplication.Provision();           // Provision it into web farm           

                using (var mySiteCollection = newApplication.Sites.Add("/", "Site 3", "Site 3 Decscription", 1033, "STS#1", "In-Wai-Svr2\\Administrator", "Administrator", "[email protected]"))
                {
                    using (var rootWeb = mySiteCollection.RootWeb)
                    {                        
                        // Code customizing root site goes here                        

                        using (var subSite = rootWeb.Webs.Add("Site3.1", "Site 3.1", "Site 3.1 Description", 1033, "STS#1", true, false))
                        {                            
                            // Code customizing sub site goes here
                        }                        
                    }
                }
            }
            catch(Exception ex)
            {
                ;
            }

It works fine i.e. it creates the web application on the specified port with sub site but this sub site will not be shown under Sites menu of Quick launch bar also it will not be shown as a separate tab on the Home Page. Is it possible to do it programatically?