Has the order already been charged? If it has you will either have to refund the customer the discount amount or give them a gift certificate towards their next order.
If it hasn't been charged yet you will manually have to discount the order before charging, and than place in "Special Instructions" that the order was discounted.
I do not believe there is a way to change the order to reflect a discount in the pricing on the order itself.
One other way you could do this is to manually reenter the order in

with the discount and delete the first order.
Somebody else may have more experience with this, we manually adjust orders for discounts that have been added after the order was placed.