I'm not all that familiar with using PHP's built-in session functions, but I would think the difference would be this:
By using the session_register function, you register the variable values and make them available as long as the session stays open.
By manually changing the values in the $_SESSION array, the values will only be set until this particular script ends. They will not be registered in the session for use when other pages are called with the same session_id.
Lacey