To apply a discount or surcharge to an invoice, first bring up the Complete sale screen.  Discounts/surcharges can be applied to individual items and/or the entire invoice. 

To apply a discount or surcharge to the entire invoice, click on the Discount / surcharge button. 

Select  manual discount or manual surcharge from the list. 

Select whether it is a dollar amount or percent discount / surcharge.  Then enter the amount and a reason for the discount or surcharge. 

Select Update price button. 

To make discounts or surcharges for individual items in an invoice, click on the relevant line item.

Here you can edit the Price per unit, Quantity, Credit work to and Discount / Surcharge.  When you're done, click Update price.