How do I edit the php code to add a custom menu?

You don't need to do anything - once you create a menu, assign it to menu position 1 (in the custom menu page)
menu 1 = %pages
menu 2 = %cats
so where you put %pages in the 'Configure Header Area' option is where the menu you assigned to menu 1 will go.

What if it is a plugin?

what if what is a plugin? teh custom menu? I'm assuming you are using the Wordpress custom menus