If you are receiving payments from the customer in response to the invoice it should be recorded as follows.

1. Choose Receive Payments from the Customer menu.
2. Choose the date of the payment made.
3. Then choose the customer who made the payment.
4. Select the Payment mode(Cash, Cheque or Credit card).
5. Choose the bank account to deposit the amount. If you are not depositing to any of the bank listed then leave the field empty. The amount will be debited to Cash in hand.
6. Then select the invoices for which the payment is to be made by clicking the checkbox near each invoice.
7. Click Save to save the payment.