There are three ways you can add a discount to an order or invoice:
Add a new line item in the order, called "Discount" and set it as a negative price.
Adjust the order total to the new price. The only downside with this option is that your client won't see the discount.
Add a "payment" to the order with the "payment type" set to "Credit."
Here's a video that shows each of these three options: