Acquia Drupal 6 Multisite
Assuming you have your web server (Apache, etc) pointing both sites correctly to your docroot, then Drupal will automatically route requests to the correct folder (and settings file) for each domain. 

If you want to have it ignore the default folder and its settings.php file, you can delete the existing "default/" folder and create a symbolic link to one of your other two sites. For example:

ln -s alumni.something.edu default


and all requests to your docroot that don't match a domain in your multisites folder will be sent to alumni.something.edu (or whatever you prefer).