If you allow credits on Invoices in the OE Company Profile, you can ship a negative quantity of an item.

To see how this would work, set up a non-stock item for the discount with a value of $1.
To give a $20 discount, enter -20 shipped and you will see the value of -$20.

Of course, you can also use the discount on the totals page to enter a discount amount.

Does that give you what you need?