In each product's data, add an array of 'attributes' which has the attribute ids as keys and the option ids or values as values.
<?php
$nid1 => array('nid' => $nid1, 'qty' => $qty1, 'discount' => $discount1, 'attributes' => array(
$aid1 => $oid4,
$aid2 => $oid2,
),
?>
Joined: 08/07/2007