I presume you are referring to our PayPal Pro or Authorize.Net checkout pages? At the moment, you can at least upload a custom logo/header image (Seller Admin > Edit Profile > Upload Your Logo button) which would appear at the top of those checkout pages. To become eligible for that bonus feature, you must first post post your E-junkie Reseller link code to a live Web site page:
http://www.e-junkie.com/ej/reseller.htm
All other checkout pages are controlled by the payment processors themselves, so we have no influence from our end as to what those pages look like (aside from providing your logo/header image for processors who support that), although you may have some options for that within your account settings on their system.
If we ever do add support for customizing the checkout pages we do control directly, I think it would most likely be a matter of allowing you to provide some CSS that could be applied to that page, although I cannot say if nor when we may add that feature.
To customize our Add to Cart, View Cart and Buy Now button images:
http://www.e-junkie.com/ej/help.customization.htm#button
To customize the Checkout buttons inside our cart display:
http://www.e-junkie.com/ej/help.custom-cart.htm