If you are selling downloads and not already an experienced programmer, we recommend NOT using the Common Thank-you Page URL setting in our Seller Admin, so you can instead rely on our standard thank-you page that provides each buyer's unique download link automatically.
You should not need to add any tracking code to your thank-you pages, since ClickBank tracks affiliate conversions during their checkout process automatically. Please see our ClickBank integration page to set this up properly, including our Thank-you Page URL you'd need to set up at ClickBank's end:
http://www.e-junkie.com/ej/selling-with-clickbank.htm
Note that if you are using ClickBank for their affiliate system, you would ONLY want to accept payments with ClickBank, since buyers who checkout using PayPal or other methods would not earn ClickBank affiliates any commission for their referral. I think ClickBank can allow a PayPal payment option during their own checkout process, so you'd want to set that up at their end, and disable PayPal at our end by going to Seller Admin > Payment Preferences to UNcheck both PayPal Standard and PayPal Pro.