The example above is showing a customer has a 1% Net 30 payment term. The first invoice Oct 15 has a discount date of Oct 25 (10 days). The same 10 days is true for the second invoice.
It will also show you a box “ This customer has discounts available. To apply discounts, click Discounts & Credits” which ask you to click the green “Discounts And credits” icon at the top.
Since the above payment date is Dec 25, the first invoice discount has expired. Highlight the second invoice without check marking it, then click Discounts And Credits icon:
Terms & Suggested Discount are shown. Select the Discount Account from your income type chart of accounts, and Discount Class if you use one. Using the income type account will reduce your sales income as it is a discount to sales invoices.
Click Done and you will be brought back to the Receive Payments window:
Now the discount is applied to the second invoice, reducing the payment amount. Checkmark the invoices to be paid (both invoices in the example above) and click Save & Close to save your work.