Here is the hack-y way that I did this straight with PHP. There are three related tables. I was using color and size as my attributes.
My parent products (configurable) don't actually exist in my catalog. They are essentially model level and then the products are the SKU level.
So LIKE 'parentproductsku%' works out for the children.
$query1 = "SELECT * FROM mage_catalog_product_entity WHERE type_id= 'configurable'";
//Find the parent id
$statusMessage = "Ok, found a product with a confgurable attribute";
$result1 = $this->runQuery($query1, "query1", $statusMessage);
while ($row1 = mysql_fetch_assoc($result1)) { //entering the first loop where products are configurable
$this->parentId = $row1['entity_id'];
$this->parentSku = $row1['sku'];
echo "The SKU was $this->parentSku" . "<br />";
//insert these into the link table for association
$query2 = "SELECT * FROM mage_catalog_product_entity WHERE type_id= 'simple' AND sku LIKE '" . $this->parentSku . "%';";
// find the child ids that belong to the parent
$statusMessage = "Found some children for $this->parentSku";
$result2 = $this->runQuery($query2, "query2", $statusMessage);
while ($row2 = mysql_fetch_assoc($result2)) {//entering the second loop where SKU is like model sku
$this->childId = $row2['entity_id'];
$this->childSku = $row2['sku'];
echo "Now we're working with a child SKU $this->childSku" . "<br />";
//"REPLACE INTO catalog_product_super_attribute SET product_id='".$product->entity_id."', attribute_id='".$attribute->attribute_id."', position='".$position."'";
$query3 = "REPLACE INTO mage_catalog_product_super_attribute (product_id, attribute_id, position) VALUES ('" . $this->childId . "', '76', '0');";
$message3 = "Inserted attribute for color for ID $this->childId SKU $this->childSku";
$result3 = $this->runQuery($query3, "query3", $message3);
$query4 = "REPLACE INTO mage_catalog_product_super_attribute_label (product_super_attribute_id, store_id, use_default, value) VALUES (LAST_REPLACE_ID(), '0', '0', 'Color');";
$message4 = "Inserted attribute for Color SKU $this->childSku ID was $this->db->insert_id";
$result4 = $this->runQuery($query4, "query4", $message4);
$query5 = "REPLACE INTO mage_catalog_product_super_attribute (product_id, attribute_id, position) VALUES ('" . $this->childId . "', '529', '0');";
$message5 = "Inserted attribute for Product Size SKU $this->childSku";
$result5= $this->runQuery($query5, "query5", $message5);
$query6 = "REPLACE INTO mage_catalog_product_super_attribute_label (product_super_attribute_id, store_id, use_default, value) VALUES (LAST_REPLACE_ID(), '0', '0', 'Size');";
$message6 = "Inserted attribute for Size SKU $this->childSku ID was $this->db->insert_id";
$result6 = $this->runQuery($query6, "query6", $message6);
$query7 = "REPLACE INTO mage_catalog_product_super_link (product_id, parent_id) VALUES ('" . $this->childId . "', '" . $this->parentId . "');";
$message7 = "Inserted $this->childId and $this->parentId into the link table";
$result7 = $this->runQuery($query7, "query7", $message7);
$query8 = "REPLACE INTO mage_catalog_product_relation (parent_id, child_id) VALUES ('" . $this->parentId . "', '" . $this->childId . "');";
$message8 = "Inserted $this->childId and $this->parentId into the link table";
$result8 = $this->runQuery($query8, "query8", $message8);
} //end while row 2 the child ID
} //end while row 1 the parent id