How about something like this:

1. /aut/index.php
Code:
header("HTTP/1.1 301 Moved Permanently");
header("Location: ../shop/index.php?main_page=index&ref=aut");
(or maybe use a full complete URL instead of the .. )
And, of course ref=aut could be ref=unitedway or whatever you plan to use later in your code.
In step 3 you'll see that this is also used as an auto-redeem coupon code by setting the 'cc_id' session variable.

2. /shop/includes/auto_loaders/config.referral_tracking.php
Code:
<?php
/**
 * @package initSystem
 * @copyright Copyright 2003-2007 Zen Cart Development Team
 * @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
 * @version $Id: config.referral_tracking.php 2006-03-06 drbyte $
 */
  $auto Load Config[100][] = array('autoType'=>'init_script',
                                 'loadFile'=> 'init_referral_tracking.php');
?>
(remove the spaces in auto Load Config before saving)

3. /shop/includes/init_includes/init_referral_tracking.php
Code:
<?php
/**
 * initialize referral-tracking-system variables
 * Determines which referral code the customer came in on 
 *
 * @package initSystem
 * @copyright Copyright 2003-2007 Zen Cart Development Team
 * @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
 * @version $Id: init_referral_tracking.php  2006-03-06 drbyte $
 */
// Determine which 'ref' code was used
if (isset($_GET['ref']) && $_GET['ref'] != '') {

  // Set the 'referral_code' session variable for reference later
  $_SESSION['referral_code'] = $_GET['ref'];

  // Use the ref code and set it to be the redeemed coupon code (add // before next line to disable this option)
  $_SESSION['cc_id'] = $_GET['ref'];
}

?>
4. In your template, call the appropriate header image based on whatever $_SESSION['referral_code'] contains.