How do apply a payment to invoices?

Welcome to Community, @elb22.

You can received the payments then it will be apply to your invoices.

Here's how:

1. On your left navigation pane, click on Sales then Select Invoices.
2. Click on the open invoice that needs to apply the payment.
3. Under the amount, click on Receive payment.
4. Once done click Save.

I also include these article as a guide:

• Record invoice payments in QuickBooks Online
• How to Record Invoice Payments

You can also Record a customer refund in QuickBooks Online.

For any confusion, just post a commend and I'll be here to answer.