How do you tell the server to use the 'site' folder as the main folder? htaccess?
If you use a hosting panel then inside the "Domains" section there should be a spot to tell each domain (and subdomain) where to located the root directory on the file server.
If you're trying to do it directly on the Apache HTTP web server then you will need to edit the httpd.conf or vhosts.conf file and change the VirtualHosts. If you run into and issues there are many people here who can answer any questions about the VirtualHosts (or Control Panel).