You can
configure a surcharge for shipping methods, but I believe that out of the box there is no function to discount some shipping methods.
I think you need a custom module that will apply a discount on the order when the shipping method is selected.
Here is an article on creating such a module (you will need a bit more logic as the discount should apply on the shipping cost, not the order subtotal):
http://devs.x-cart.com/en/changing_store_logic/creating_global_discount.html