If you are using E-junkie-provided purchase-button codes you do NOT need to manually configure PayPal IPN at all. When a buyer takes an order from our buttons/cart to PayPal for checkout, we automatically include our IPN URL along with the order data.
If you are using E-junkie's built-in Affiliate program, any Affiliate who referred the sale via their link would get credited for the sale automatically. See here for more information on how our Affiliate programs work and the different link types:
Also, we recently added some new Common Affiliate Program Settings in Admin. These allow you to configure an across-the-board commission percentage and issue just one common Hop Link to each Affiliate for all of your products, and you can also specify the URL of a page on your site to which Affiliates could refer for more info/instructions. Any product-specific Affiliate link settings would take precedence over the "default" Common settings, and if you delete product-based Affiliate settings while having Common settings, any old Hop Links issued would continue to work as equivalent to a new Common Hop Link.