Payments can be added in the billing & expense tab under client. Click on "add invoice item". In the cost section, put a Negative sign in front of the cost and the system will know it's a payment instead of a charge. See below. Then approved the item and you can add it to the invoice by going to the invoice tab, clicking on the "edit" icon, click on the checkmark next to the item you want to add to the invoice and then hit submit.