How to get rid of auto generated classes in secondary menu links and add my own classes
You can use this preprocess hook to modify the menu classes.

For example, modify the output of the secondary menu links like this.

function YOURTHEME_links__system_secondary_menu(&amp;$variables)
{
   $output = "";

   foreach ($variables['links'] as $item =&gt; $link) {
      $classes = array('class1', 'class2');
      $output .= sprintf('&lt;li class="%s"&gt;%s&lt;/li&gt;', implode(' ', $classes), l($link['title'], $link['href']));
   }

   return $output;
}