Hi there, LandR.
I have a few questions before we proceed. Are you manually trying to record a payment in QuickBooks Online, or are you looking to match your bank transactions, given that the transactions are already in your bank feed?
If you are trying to match a discounted ACH payment to an invoice, you can select the Match option in the Bank Feeds to link them together for a partial payment of the invoice. To mark the invoice as fully paid, you can add the discount as an individual line item with a negative rate and a description.
For example, since your customer made their payment within 10 days, they get a 2% discount. You can add Early Payment as a service item, then enter a rate in a negative (-) amount. To reuse this discount later, select the item and then select + Add new option.
Here's a visual reference you can refer to:

This thread remains open if you meant something else. The Community team is here to help out.