Most likely, I'm going to guess you want to change the html output of the menu, correct? If that's the case, you'll use a theme function in your template.php file to override the original menu html. The two functions you'll use are:
If you're not sure how to use theme functions, I may do a videocast on that this week over at the Mustardseed Podcast.
this is probably a really stupid question, but I've been searching all over the web for what i would think should be a pretty simple issue. I am trying to customize the way drupal output's it's menu. If someone could please help with how to customize this that would be awesome.