using theme_menu_link() I am currently using theme_menu_link() but it themes every menu in Drupal. I only want to theme my main menu. How can I check for a specific menu?

function theme_menu_link(array $variables) {
  $element = $variables['element'];
  $sub_menu = '';

//if(id == main_menu){ theme it different } 

  if ($element['#below']) {
    $sub_menu = drupal_render($element['#below']);
  }
  $output = l($element['#title'], $element['#href'], $element['#localized_options']);
  return '&lt;li' . drupal_attributes($element['#attributes']) . '&gt;' . $output . $sub_menu . "&lt;/li&gt;\n";

}
You can get the ID of a menu by looking at the URL when you edit it in the menu configuration admin interface and converting dashes to underscores.

For example, on admin/structure/menu if I hover 'User Menu' I see admin/structure/menu/manage/user-menu/edit which means that the menu machine name is 'user_menu'.

The $element contains the menu's id: $element['#original_link']['menu_name']. 

So you can put that in your if() and get

if($element['#original_link']['menu_name'] == 'user_menu') {
  ...
}


where you replace 'user_menu' with the name of the menu you want.