add_associated_product.php

<?php
include_once 'magento/app/Mage.php';
Mage::app();

$childproduct = Mage::getModel('catalog/product')->loadByAttribute('sku','red');
$parentproduct = Mage::getModel('catalog/product')->loadByAttribute('sku','mytestsku');

function _attachProductToConfigurable( $_childProduct, $_configurableProduct ) {
   $loader = Mage::getResourceModel( 'catalog/product_type_configurable' )->load( $_configurableProduct );
   $children = $_configurableProduct->getTypeInstance()->getUsedProductIds();
   $children[] = $_childProduct->getId();
   $children = array_unique($children);
   $loader->saveProducts($_configurableProduct, array_values($children));
}

   //$ids = $_configurableProduct->getTypeInstance()->getUsedProductIds(); 
   //$newids = array();
   //foreach ( $ids as $id ) {
   //   $newids[$id] = 1;
   //}

   //$newids[$_childProduct->getId()] = 1;

   //$loader->saveProducts( $_configurableProduct->getId(), array_keys( $newids ) );                


_attachProductToConfigurable($childproduct, $parentproduct);