It happens sometimes that your clients pay with a higher amount than the invoice balance and your client would prefer keep the amount as credit for futurs jobs.
To process that type of payment:
Click on the button "Pay" of "Payment schedule" on the invoice to pay manually
Pay the amount you receive for the invoice with a explicative note
Go back to your "Payment schedule" and click on "edit"
Enter the modifications in the window "payment details" and write the explications in "note"
Your invoice will now show the right amount received and the balance that needs to be refunded or credited. You can send a receipt to your client if you would like.
For the refund, go to the "Action" button and select "refund"
Notes
If you are connected to accounting system, make sure to reimport the invoice with the changes.
The reports will display all the changes