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Any payment not already applied to an invoice can be settled to one or more open invoices.
To settle a payment, display the list of payments by hovering over the Finances menu and selecting the Payments & refunds option. Now, either click the Settle button beside the payment in the list...
...or click the payment within the list, then click the Settle button from the payment details.
From the Payment settlement screen, enter the amount to be applied to one or more open invoices then click the Settle button beside each invoice.
You do not have to apply the entire amount of the payment. If you apply the full amount of the payment to invoices, then the payment will be marked as fully settled.
Otherwise, the payment will be marked as partially settled.