<p>How do you specify the Fill Factor when creating an index in MySql?</p>

You don't.
http://dev.mysql.com/doc/refman/5.0/en/create-index.html
However, it is an 'accepted' feature request for version 6.x:
http://bugs.mysql.com/bug.php?id=18178
So, don't hold your breath on seeing it any time soon.