If you are receiving payments from the customer in response to the invoice, the transaction details should be recorded as following.

1. Choose Receive Payments from Customer menu.
2. Choose the date on which the customer has made payment.
3. Then choose the customer who made the payment.
4. Select the Payment mode (Cash, Check or Credit card).
5. Choose bank account to deposit the amount.
6. To keep the "Cash In Hand", don't select any option.
7. If you want to keep the cash in a fund to deposit later, select Group with Undeposited Funds.
8. Then select the invoices for which the customer has made the payment by clicking the check box adjacent to each invoice.
9. Click Save to save the payment.