Commerce Kickstart demo: How do I change the region for the blocks Main Menu and Secondary Menu?
Menus are printed in the region--menu.tpl.php @ profiles/commerce_kickstart/themes/commerce_kickstart_theme/templates .

You can see the settings for the same in the link admin/appearance/settings/commerce_kickstart_theme



If you would like to change the positions of menus, then disable the Main Menu &amp; Secondary menu in above link settings as shown in screenshot and enable the blocks using Blocks page.