QuickBooks Online is equipped with tons of helpful and easy-to-use tools to assist you in your business bookkeeping. I know how important it is to be able to clear out any outstanding balances caused by overpayments. I'd be happy to explain what you can do if your customer overpaid by $0.01.
When you record the payment towards your invoice, you'll enter the total amount paid to you by the customer. If your customer overpaid by $0.01, this will generate a customer credit, which you'll then be able to put towards their future purchases. If you want to make sure the credit is automatically applied on their next bill, click the Gear icon > Account and Settings > Advanced > Automatically Apply Credits = ON.
If you won't be conducting any future business with this client, you can clear it by recording it as a refund. To do this, follow these steps:
Select + New.
Select Refund receipt or Give refund.
Select the Customer ▼ dropdown, then select the customer you want to refund.
Select the Refund From ▼ dropdown, then select the bank you deposited the payment for the invoice too.
Add all products or services the customer returned in the Product or service column.
Make sure to fill the quantity, rate, amount, tax, and other fields accordingly, then select Save and close.