Well depends on wich checkout process you have used, on some sites i had to make a custom checkout for bank deposits so i made a page that after the user registers the deposit i send him to a thank you page with a message about the days it takes to confirm the order but on this page i have a hidden code to empty the order session and the cart, this is what i do on the top of the page in code view i add manually
<?php
//WA eCart Include
require_once("WA_eCart/CartName_PHP.php");
?>
<?php require_once("Connections/myconection.php"); ?>
<?php
$cartName->GetContent();
?>
and at the end just before the </body>
i add
<?php
$cartName->ClearCart();
unset($_SESSION['OrderSessionName']);
?>
Let us know if it was helpfull :p