Hello,
If you just need to add the new pager, please do the following:
$pager = $docx->addPageNumber('numerical', array('jc' =>'center', 'rawWordML' => true));
$myFooter = $docx->createWordMLFragment(array($pager));
$docx->addFooter(array('default' => $myFooter));
This is, after create the pagenumber get the WordMLFragment and and it to the footer.
If you want a further integration we recommend you to upgrade to phpdocx 4.0.
Regards.