Can I add a credit card fee that is a percentage of the total order to a storefront?

We don't have cart-based pricing - which is what you need to add a percentage fee to an order.  We also don't have the ability to change pricing based on the payment method used.  You would need to adjust your pricing on the product level if you want to add percentage fee to cover your credit card processing fees.  This price will apply regardless of the payment method.  Note that you can add a mark up on the Pricing tab of the product without needing to adjust the pricing engine.