IPN stands for Instant Payment Notification. It's a back-end data transmission that PayPal sends to another system to confirm when a payment has completed for an order, which also passes along the order data itself (who bought what for how much, etc.).
IPN settings in your own PayPal account tell PayPal where to send these IPNs for any payments you receive. E-junkie's Cart and Buy Now buttons tell PayPal where to send us an IPN for each order we send to them for checkout, and our IPN specs would override the manual IPN settings you have in your PayPal account; this means we get the IPN from PayPal for those sales, instead of whomever you'd specified in your PayPal account's IPN settings.
If you still needed that third party to receive IPNs for all your E-junkie sales, you would need to add their IPN-receiving URL in your E-junkie account's Seller Admin > Account Preferences > Common Notification URL setting (a product-specific setting is also available). As stated previously, this would only work if that third party does not need to validate IPNs with PayPal, and if they can handle or ignore some extra data we add to the standard IPN format, so you should ask them for clarification on this matter and probably refer them to our Integration documentation here:
Now, here's a really neat thing: Regardless of which checkout method your buyers use (PayPal, Authorize.Net, etc.), we are always informed of the sale, and our Integration feature can still forward the order data to any URL you require as an IPN-style submission. This allows us to send imitation PayPal-style IPNs to third-party services that require IPN... even if you are not accepting any payments by PayPal at all!
Now, about paying your affiliates:
After the end of each calendar month, you would go to E-junkie Seller Admin > Pay Your Affiliates to generate a "masspay.txt" file for the last completed month. This summarizes lump-sum commission earnings for each your affiliates who earned commissions in that last completed month.
This is a plaintext file in a fairly simple, standard format, so you can open the file in a text editor like Notepad, or in a spreadsheet program like Excel, and simply use that as a reference to pay affiliates by whatever means you wish.
However, if you want to make paying affiliates really easy, you can simply upload the "masspay.txt" file to PayPal Mass Payments to pay all your affiliates automatically in one fell swoop! You don't even have to accept PayPal payments from buyers to do this, just as long as you have a PayPal account yourself. Affiliates who don't have a PayPal account will receive an email notifying them of the payment and inviting them to start a PayPal account in order to claim the payment.