Short answer: the web root should be pointing to the index.php in the Drupal root for all of the sites you're hosting on that codebase.
In your case, you are getting an error because there's nothing in the /sites/yoursite.com directory that your webserver can run on it's own.
Longer answer: Configuring Drupal for multiple domains takes a little bit more reading and learning that can be summarized in an SO response.
The guide at http://drupal.org/getting-started/6/install/multi-site is a great place to start, and includes links to videos and additional tutorials in case you need additional help.