Hello Steve.<br />
Your custom build cart can see if the URL contains an affiliate parameter or not. If it does, it can fill the promo code field for the user automatically.<br />
Alternatively your cart could offer an option to send the promo code as it's own URL parameter. For example like this: &promo_code=1234 and when the visitor lands on your website with such parameter in his link your cart saves the field value in a cookie which will then populate the promo code field during the checkout automatically.<br />
All this is cart functionality. It's not really related to our tracking software and it's tracking in any way.