I went to Appearance -> Menus -> Edit Menus and created a custom menu there. Then under Menus -> Manage Locations is says:

Your theme supports 2 menus. Select which menu appears in each location.

and there is the choice between Theme Location -> Menu 1 and Theme Location -> Menu 2.
Its not clear what these are, but in Atahualpa Theme Options -> Header Area there are tabs for MENU 1 (Page Menu) and for MENU 2 (Category Menu). Since I use MENU 1 as my main menu for most pages, I wouldn't want that to be changed. If under Theme Location -> I set Menu 2 it does not actually seem to show up in Atahualpa and the options in Athahualpa for Menu 2 still appear to be those for Category Menu and have no connection to the custom menu I created.

Second, isn't there some way to add more than just an extra menu? I would ideally like to be able to have several custom menus which I use on different pages.

I also have looked at creating a custom page template for Atahualpa but contrary to the Wordpress standard documentation there is no actual page.php and searching did not find anything. Ideally it would be nice to have several page templates with each one using a different custom menu.

Please don't double post - it wastes our time. Sometimes post are heald for moderation.

page templates can be made by copying index.php - name it what you want and customize it. Take a look at the included 'template_multi_column_custom_query.php' as an example.