Let\'s say we have the following menu structure:
menu #1
menu #2
menu #3
- submenu #1
-- subsubmenu #1
-- subsubmenu #2
-- subsub
You can use the order by menu_order
parameter for your query, and having a descending order to sort it out.
Note: you must use the menu_order attribute under the Page Attribute Box, at the right of the edit screen
Rewrite your query as
<?php query_posts('post_parent=12&posts_per_page=2&orderby=menu_order&order=DESC'); ?>
See: http://codex.wordpress.org/Function_Reference/query_posts#Order_.26_Orderby_Parameters