I would think you would put it in the main/order_message.tpl file. Something like this:
Code:
{literal}
<head>
<SCRIPT LANGUAGE="JavaScript">
<!-- Overture Services Inc. 07/15/2003
var cc_tagVersion = "1.0";
var cc_accountID = "xxxxxxxxxx";
var cc_marketID = "0";
var cc_protocol="http";
var cc_subdomain = "convctr";
if(location.protocol == "https:")
{
cc_protocol="https";
cc_subdomain="convctrs";
}
var cc_queryStr = "?" + "ver=" + cc_tagVersion + "&aID=" + cc_accountID + "&mkt=" + cc_marketID +"&ref=" + escape(document.referrer);
var cc_imageUrl = cc_protocol + "://" + cc_subdomain + ".overture.com/images/cc/cc.gif" + cc_queryStr;
var cc_imageObject = new Image();
cc_imageObject.src = cc_imageUrl;
// -->
</SCRIPT>
</head>
{/literal}