How to use hook_menu to add an item to the secondary links?
You can use menu_name to specify the menu of the items you are adding:

See the hook_menu docs for more info.

For example, to add the item to the main menu:

function hook_menu()
{
    $items = array();
    $items['bla'] = array(
        'title' =&gt; 'bla',
        'page callback' =&gt; 'mymod_blah',
        'expanded' =&gt; TRUE,
        'menu_name' =&gt; 'main-menu',
    );
    return $items;
}