I’m not sure what you mean with ‘…i use the web site it will link’…
Your website (a bunch of text-documents and images) is stored in a folder of your webserver. The webserver is linked to the app-server (i .e php image). Each php statement ( marked with <?php and ?>) will then be send through port 9000 (if correctly setup in nginx.conf) to you app server. The return-value then can be displayed on your website.