In Omega in region--menu.tpl.php we have this line which renders the main menu...

print theme('links__system_main_menu', array('links' => $main_menu, 'attributes' => array('id' => 'main-menu', 'class' => array('links', 'inline', 'clearfix', 'main-menu')), 'heading' => array('text' => t('Main menu'),'level' => 'h2','class' => array('element-invisible'))));

In my template.php file, I have --

function THEME_menu_tree__system_main_menu($variables) { ... }
function THEME_menu_link__system_main_menu(array $variables) { ... }

However, this does not seem to hook into the menu before it's rendered.

Any suggesions?

Ultimately, what I am trying to do is display the sub-links in my main menu which seem to be hidden by default in the Omega theme.

Thanks