Products are not linked to any particular payment processor in E-junkie Seller Admin; the payment method(s) available for any given product is determined by the Cart or Buy Now button(s) you choose to copy and paste into your site for that product.
You can bundle any download products that appear in the list when you enable "Package files from other products" in the bundle product's settings.
BTW, on the site where your buyers arrive via CB affiliate links, there should be no way that CB affiliate-referred buyers could purchase anything from you without using ClickBank; i.e., if you're selling any products without ClickBank, you should be maintaining a separate site or page for those, which CB buyers cannot readily get to.