Adding a Discount as a Line Item
This article shows how to add a flat discounts to sales orders. This can be done by creating an item from a item group that doesn't count inventory like a non inventory item or other charge with price valued at zero.
If your not sure how to create an item refer to this article: Create an Item
Once you have you have the discount item created, you can use it as a tool to reduce the balance on a sales order by changing the price of the discount line item to a negative number that will adjust the amount as needed.
If you are looking to use a more conventional discount refer to: Discount