From your Services section of your inventory, click 'Add Service'.
Then, click 'Discount Service'.
From here, you can create your discount to operate how you like (flat fee, percent of order, or percent of line item group).
Please note: a discount service set as "Percent of Line Item Group" or "Percent of Order" will not discount other services with the same pricing structure. For example, a 10% discount service will not subtract from a 10% service charge.