Amanda, have you looked at this page: http://drupal.org/node/15365
You should be able to make the rewrite rules needed by Drupal apply only to the directory in which Drupal resides. I think that was the point of Andrew's post about using .htaccess. You probably want to use the Apache <Directory> section.
Actually, using .htaccess is less efficient than putting the same directives right in Apache's config file, and is normally only necessary when one cannot edit the Apache config file.
-- ..chrisxj