Hi maw444, thanks for posting on the Community.
If you already have the unapplied payment on the customers account, you can apply this to the invoice by selecting Receive payment > Tick the payment under Credits on the Receive Payment screen. This status of the invoice will then show as partially paid with a new balance due amount. To send this to your customer, select Edit beside the invoice from the customers transaction list > Save & send.
If you don't already have the payment on account, you can record this by selecting New transaction on your customers account > Payment. Fill in the details as you see fit, and enter the amount received in the amount field. When saving, if no transaction is selected under 'Outstanding transactions' to apply the payment to, a pop-up message will appear to confirm to save as a credit.