We would recommend using our built-in affiliate system rather than any third-party affiliate solution, as we can ensure that referrals and conversions are tracked as reliably as possible through our backend system without depending on thank-you page visits or conversion tracking code/pixels -- see this help page for details:
http://www.e-junkie.com/ej/help.affiliates.htm
That said, if you still prefer to use your third-party affiliate solution, you can add any tracking code you wish to your E-junkie-generated thank-you pages. To add the same tracking code to all pages regardless of the item(s) purchased, you can put this in your Seller Admin > Account Preferences > Common Thank-you Page HTML. To add different tracking code depending on the item(s) purchased, you can put this in the Message (HTML) field of each product's settings. The iframe, javascript, or img should all work fine, so take your pick.
Bear in mind that conversion tracking method may be unreliable if you are not selling downloads, for the reasons we explain here:
http://www.e-junkie.com/ej/faq.tracking.conversions.htm
If you're selling tangible goods, we have a workaround to improve reliability of that conversion tracking method here:
http://www.e-junkie.com/ej/tips.tracking.conversions.htm