If you are using E-junkie with ClickBank, you would actually use E-junkie's Buy Now button code for ClickBank, which you would obtain from your E-junkie Seller Admin. As long as the buyer checks out through ClickBank, that should track your CB affiliate referral commissions, and using the E-junkie-provided button code is necessary for our system to process the sale after checkout.
Once you get your product approved with ClickBank, you would change the product's settings at CB's end to use your E-junkie thank-you/download page URL rather than the token download page you'd set up initially just to get the product approved. Our ClickBank integration page gives full instructions; just follow these and you should be fine:
http://www.e-junkie.com/ej/selling-with-clickbank.htm