Go to System profile. Select profile = OM: Discounting Privileges and set value to "Full" or "Unlimited" (Depend on your need)So let try entering S.O. You just enter it as normal. for each order line, just click "actions" button and then select "Edit Price Adjustment" Now you can enter number of % discount in "Rate" field. Then click "Apply" button.
Next, setup % discount modifier. Don't forget to select "Automatic" and "Override" check box. For this step you can set as dummy discount modifier and set % rate = 0