When looking at the template files for Magneto, things can seem very confusing. Especially when your talking about the navigation. For example if you try to add a menu option to the top menu, you would expect to find an array or some sort of call to the database. However, in app/design/frontend/default/YOURTHEME/template/page/html/header.phtml there is only a php code <?php echo $this->getChildHtml('topMenu') ?>.
Unless your savvy enough to understand whats happening, that is a reference to some xml. This xml is what sets the values for that menu.
So, how are we supposed to add things to that menu? There are lots of bad advise out there saying you can just write your own, or get that list of values and hard code your own...but its so much easier than all of that.
The best way is to create or edit your local.xml