Use the WordPress Menu... ADMIN>>>APPEARANCE>>>MENUS
Takes a little time to get right but well worth it because you can mix and match categories and pages (plus custom menu items) as required.
You will see that you have TWO menus available to configure in Atahualpa 3.5.3
Add all of the items for each menu (Menu 1 and Menu 2) by ticking the boxes in the left column as required and then you drag and drop into position on the right of the Wordpress Admin Menu page with the positioning (the amount each menu item is "tabbed" indicating its level in the menu).
The ability to change menu orders easily is a huge benefit of using the Wordpress menu system.
All new items added to a menu will appear at the bottom of the list and can also be dragged and dropped.