How the "subdomain" is treated is really up to you. You could easily have your DNS server resolve any "subdomain" to the same IP address of the core domain, or you could set subdomains to resolve to different IP addresses.
The "sub" part of the subdomain is just a host header. The domain is supposed to be the actual host. You can serve different sites using subdomains by setting up different sites in your web server (apache/ IIS, etc).
I am assuming you are speaking of Google's Webmast Tools ...
When you initially set up the site(s) using Google's Webmaster Tools, you actually have the option to treat all subdomains as part of the same domain, if you wanted it to work that way. Take a deeper look at the Google Webmaster Tools, Go into the main site (
www.site.com), go to site configuration -> settings. Look under Preferred domain.
Here is Google's help link
http://www.google.com/support/webmas...er=44231&hl=en
Hope this helps answer your question.