OS X Server: How/where is the server app changing the Apache configuration?

When I view the "Websites" section in the OSX Server app, I am able to manage what appear to be virtual hosts. However, when I go to check Apache's vhosts configuration, there doesn't seem to be anything configured. Is there some kind of magic going on here, or are the changes made via the Server app affecting files somewhere else? Can anyone shed some light on how OS X manages the built in Apache installation?

Since you mention Server App, I assume your OS X is Mountain Lion. The actual apache config is at the following location

/Library/Server/Web/Config/apache2/

Virtual host config is in

/Library/Server/Web/Config/apache2/sites

You are probably looking at /private/etc/apache2/ or /etc/apache2/, which is not being used.