If your objective is to set up an affiliate program, you may be interested in our built-in affiliate system that can track referrals, conversions and commission earnings automatically through our back-end without relying on thank-you page visits:
http://www.e-junkie.com/ej/help.affiliates.htm
You can add custom HTML (such as tracking code) on a product-specific basis by pasting it into the Message (HTML) field of the relevant product's settings. If a buyer orders more than one item, your Message (HTML) for each product ordered will be added to the buyer's thank-you page. This help page explains more about thank-you page customization:
http://www.e-junkie.com/ej/help.custom.thankyou-page.htm
Since you are using PayPal and not selling any downloads, you can have PayPal automatically redirect buyers to your E-junkie-generated thank-you page when they complete checkout. First, go to your E-junkie Seller Admin > Payment Preferences and UN-check "Wait for pending payments...", then go to your your PayPal account Profile > More Options > My Selling Tools > Website Preferences, where you should set both Auto-Return: ON and Payment Data Transfer: ON and provide this as the Return URL:
https://www.e-junkie.com/ecom/rp.php
(Note to any download sellers who may read this post: The instructions in the paragraph above will interfere with our ability to provide download links to buyers immediately following checkout; see this help page for further details and tips:
http://www.e-junkie.com/ej/tips.tracking.conversions.htm )
