If there is a negative balance on a customer's invoice because they overpaid their invoice, how would I fix it in QBO?

Let me help you handle overpayments and fix the negative balance on your invoice, @cbanotai.

When your customers pay you too much, we can either use the credit toward an invoice, refund the customer, or enter the overpayment as a tip in QuickBooks.

If you wish to apply the credit to an invoice already created or to a new one, here's what we need to do: 

Apply the credit to an invoice you already created

1. Proceed to the + New button
2. Choose Receive payment.
3. Select the customer, then the credit, and the invoice.
4. Choose another pending invoice and enter the overpayment amount in its Payment column.
5. Click Save and new or Save and close.

Apply the credit to a new invoice

1. Click + New.
2. Choose Invoice.
3. Create the invoice.
4. Select + New. Then select Receive payment.
5. Choose the credit and then Save and new or Save and close.

If your customer has paid you by mistake, you can simply give them a refund. Otherwise, you can record it as a tip if your customer paid more than their total intended.

Then, check to see if the negative balance on your invoice has been removed.

You'll want to put payments into the Undeposited Funds account before you combine them into a deposit. You can review this resource for detailed information: Undeposited Funds account to record the payments in QuickBooks. 

That should do it! If you have further concerns with managing overpayments, feel free to let me know. I'm always around to help.