html.tpl.php

    <?php if ($main_menu): ?>
      <div id="main-menu" class="navigation">
        <?php print theme('links__system_main_menu', array(
          'links' => $main_menu,
          'attributes' => array(
            'id' => 'main-menu-links',
            'class' => array('links', 'clearfix'),
          ),
          'heading' => array(
            'text' => t('Main menu'),
            'level' => 'h2',
            'class' => array('element-invisible'),
          ),
        )); ?>
      </div> <!-- /#main-menu -->
    <?php endif; ?>

template.php

function THEME_preprocess_html(&$variables) {
  $variables['main_menu']         = theme_get_setting('toggle_main_menu') ? menu_main_menu() : array();
}