How to add multiple taxonomy terms to node?
First of all, be sure that the taxonomy reference field exist in manage field page of your content type, then you can attach that field to your node via the function field_attach_update, before attaching that field to node let's get it from your data passed through Ajax :

 $terms = $form_state['values']['your_tax_field'];

 // attach to node :
 $node = new stdClass();
 $node-&gt;nid = $nid // Make sure that the nid exist;
 $node-&gt;type = 'your_content_type';
 $node-&gt;your_tax_field = $terms;
 field_attach_update('node', $node);
 entity_get_controller('node')-&gt;resetCache(array($node-&gt;nid));


Not tested but should work like that! You can use devel module to debug your data passed in the form.