Drupal 6x - Primary Links jquery accordion menu

Answer 1

Overriding theme functions is the most basic thing done in themes.

Short version is, that if you create a function named [theme_name]_menu_item, that function will be used to generate the html instead of the default one: theme_menu_item. So yes this can be done in your template.php.

Note, the changes will affect all menu items, not just the ones in your primary link menu.

Long version

Answer 2

What's a problem to append jquery accordeon to standard primary menu output? There's everything you need for.