Sam nailed it. When you're on the payment part of the checkout process, there's a section on the right that says:
Affiliate commissions summary
Earned affiliate commission
And below that, there's a button that says "Redeem" and you click that to apply your commission to your purchase. (Of course, you have to have some earned commissions in your account for the section to show up.)
I'm glad you were able to check out like you wanted.
EPP = Eden Partner Program. It's the same thing as the Affiliate Program, but we don't use that abbreviation around the site much anymore. I'm sorry about the confusing wording.