To the best of my knowledge, Q2A does not have "Menu Reorder" feature. There are various realization methods. I hacked core (http://www.powerqa.org/documents/core/admin-layout/). However, easiest and safest way is to make your layer plugin. Mouseover layer plugin will be helpful as an example.
public function nav($navtype, $level=null) {
if($navtype == 'main' && isset($this->content['navigation'][$navtype])) {
//$keys_old = array('activity','$','qa','questions','hot','unanswered','tag','categories','user','ask','admin');
$keys_new = array('$','qa','questions','hot','unanswered','tag','categories','activity','user','ask','admin');
qa_array_reorder($this->content['navigation'][$navtype], $keys_new);
}
qa_html_theme_base::nav($navtype, $level);
}