How to print out bootstrap menu?
In the boostrap theme there is a file 


  theme/menu/menu-tree.func.php


This file contains a function 


  bootstrap_menu_tree__primary


This function wraps the menu as following:

'&lt;ul class="menu nav navbar-nav"&gt;' . $variables['tree'] . '&lt;/ul&gt;';


So you have to give the wrapper of your menu those classes and make sure the structure is exactly the same as the primary menu.

Hope this helps you out.