Question about Google Analytics for WordPress MU

In the plugin description it mentions:

To track all your subdomains separately you’ll need to configure analytics and add in an extra line of code to the tracking code as described here (very easy to do): http://www.google.com/support/googleanalytics/bin/answer.py?hl=en&answer=55524

My question is if my WPMU site is configured to create new subdirectories instead of subdomans is this line of code still necessary to add? I just want to make sure.