How do I print a custom menu?
Have you tried using the Menu Block module (D7)?

Disable the main menu in the theme settings and create one or multiple menu blocks with a lot of options for the menus. The module can render submenu items with the main navigation and/or in a separate menu-block. The Menu block module can render a custom menu as well.

You can also add an extra region to your theme that renders a menu-block-menu inside a nav-tag:

yourtheme.info file add:

regions[nav_custom] = Nav Custom


In page.tpl.php add:

&lt;?php if ($page['nav_custom']): ?&gt;
    &lt;nav id="nav-custom" role="navigation" class="navigation"&gt;
      &lt;?php print render($page['nav_custom']); ?&gt;
    &lt;/nav&gt; &lt;!-- /.section, /#nav-custom --&gt;
&lt;?php endif; ?&gt;