There isn't a way to raise a credit note from within AGG SMART as this would need to be done within your accounts package.
However, you can match the amount of credit you are giving by applying a discount to the invoice on AGG SMART.
Use the "Check" facility by clicking the check box (Arrow#1) and into the "Additional" box, enter a negative number to match the credit as per (Arrow#2).
In the screenshot below, a -100 value has been entered into the "Additional" box. This will provide a £100 discount on the invoice to balance it.