Open the invoice and press Record payment in the Payments card. Enter the Amount received, the date it was received, the Method (Bank transfer, Card, Cash, Cheque, Online payment or Other) and an optional Reference and Note. A payment can never be more than the amount due.
The invoice becomes Part paid, and the Amount due (the total less credit notes and payments) shows on the invoice, the Invoices list, the customer's Account, their copy of the invoice, the portal and the Dashboard. It becomes Paid by itself when nothing is left to pay. Mark as paid records one payment for everything still due.
Entered a payment by mistake? Press Delete next to it and confirm: the amount is due again. A credit note on a part-paid invoice first takes off what is still due; any part above that is a refund due to the customer.