Zend_Dom_Query is tailored just for querying a dom, so it doesn't provide an interface in and of itself to alter the dom and save it, but it does expose the PHP Native DOM objects that will let you do so. Something like this should work:
$dom = new Zend_Dom_Query($html);
$document = $dom->getDocument();
$elements = $dom->query('div[id="someid"]');
foreach($elements AS $element) {
//$element is an instance of DOMElement (http://www.php.net/DOMElement)
//You have to create new nodes off the document
$node = $document->createElement("div", "contents of div");
$element->appendChild($node)
}
$newHtml = $document->saveXml();
Take a look at the PHP Doc for DOMElement to get an idea of how you can alter the dom:
http://www.php.net/DOMElement