Typically you would promote your affiliate program on your own Web site, where you would post the sign-up link code you can obtain from your Seller Admin > Affiliate Program Settings.
You can also choose to list your affiliate program in the E-junkie Marketplace; to do this, you would need to add listings for your products in an E-junkie Shop:
http://www.e-junkie.com/ej/help.promote.htm
The IPN step mentioned in our affiliate program set-up instructions doesn't actually do anything, so you won't see anything about affiliate earnings in your PayPal IPN history. We had originally thought that would have PayPal inform our system whenever you paid out commissions to affiliates, but in practice that didn't work out as intended, so we'll be removing that step from the next version of Admin. The IPN settings you added don't affect anything, but changing them could cause problems, so just leave them as they are now.
After joining your program, affiliates must obtain the link code we provide for them in their Affiliate Admin, which is necessary to track their referrals. Just making a regular link to your site won't work for affiliate tracking purposes. Your E-junkie Transaction Log will show if an affiliate referred any given sale.
Affiliate commission pay-outs are not made automatically for each sale; instead, after the end of each month you'd go to Seller Admin > Pay Your Affiliates to generate a monthly report listing lump-sum commission earnings for each affiliate in the last completed calendar month. You can upload that file to PayPal Mass Payments to pay out all commissions for that month at once, or you can just read the file as a reference to pay out commissions manually by some other method.
This help page explains everything you'd need to know about setting up and managing your E-junkie affiliate program:
http://www.e-junkie.com/ej/help.affiliates.htm
We also have a help page for affiliates, explaining our system and how to use it from their perspective:
http://www.e-junkie.com/ej/help.for-affiliates.htm