You can add a discount on an invoice either set to a Percentage or Flat fee.
First, go to Invoicing from your blue menu bar and select the invoice you would like to add a discount on. Top left you will see the Invoice Discount option. Pull down the drop down to choose between Percentage or Flat Fee and enter in your amount. You will also see "Discount Options" and if clicked it will allow you to uncheck the options to just apply the discount to Labor or Expenses only. When finished, click the Save button. After saving, at the bottom you will see the amount of the invoice after the discount was applied.