Instead of having links to categories or pages, I would like the top header bar to display the links I've defined in Wordpress' "Links" model (preferably only those with a certain category).

How would I go about doing this?

use the wordpress menu and create your own menu (dashboard->appearances->menus) on that page the menu you put in the menu1 position will show up when you use the Atahualpa %pages option in the 'Configure Header Area' option and menu2 will show up when you use %cats.

Works! Thanks!

You would just create a custom menu item in Appearance>Menus.