Integrating an affiliate software in WHMCS

[JamesN]

Hey there!
I am trying to integrate a custom affiliate software into my WHMCS.
I have added the following into header.tpl in my template:

<script type="text/javascript" src="https://www.affiliatly.com/easy_affiliate.js"></script>
<script type="text/javascript">startTracking('AF-xxxxxxx');</script>

where AF-xxxxxxx is a redacted version of the actual numbers. 
This works when I go straight to my site using https://domain/whmcs/?ref=1 or https://domain/cart.php?a=view&ref=1 - it applies a cookie to the browser. So all is well there. YAY!

However - I am using direct links for checkout. For example:
 

https://domain/whmcs/cart.php?a=add&pid=1&billingcycle=monthly&ref=1&skipconfig=1

When I follow this link - the cookie is not set. As if its completely dropping the &ref=1 portion. 
 

Is there a place where I need to add that javascript, so that will apply when using &skipconfig=1 ?
I am starting to run in circles here and would really appreciate any help that you guys can provide.

Thank you!