Discounts you configure in E-junkie Seller Admin can only be applied before checkout, not during checkout on any third-party payment processor's site.
We have no way to grant an automatic discount based on payment method, because we can only apply discounts before checkout, which is before the buyer has selected a payment method. If you are using our cart buttons, discounts would be applied in the buyer's cart before they click a checkout button.
If you are using our Buy Now buttons, you'd need to use a modified version of our Buy Now button code that will allow buyers to enter a discount code before clicking the Buy Now button, and only certain kinds of discounts can work with a Buy Now button, as explained in more detail here:
This help page gives tips for testing your setup: