Hello there, @francesb.

When you receive an overpayment on a customer's account, you'll have to use the Receive payment option to enter the actual amount paid for the invoice. Then, choose to either do a refund or keep it as a credit (only if you've set up customer credits to apply to future payments by default). You can refer to this article to learn more about this: Handle a customer credit or overpayment in QuickBooks Online.

Once you're done, deposit the payment (from the Undeposited Funds account) using the Bank deposit feature. This way, you're able to deposit the funds or the received payment in the bank. Here's how:

1. Go to the + New button.

2. Select Bank deposit.

3. From the Account dropdown, choose the account you want to put the money into.

4. Click the checkbox for the payment you've received.

5. Select Save and close or Save and new.

Then, once the payment is downloaded, match it to the existing entry in QuickBooks to keep your account updated. For the step-by-step guide, you can refer to this article: Categorize online bank transactions in QuickBooks Online.

Additionally, I'd recommend reconciling your accounts every month. This will help you monitor your income/expenses and detect any possible errors accordingly. You can check out this article for the detailed steps: Reconcile an account in QuickBooks Online.

Please don't hesitate to let me know if you have other concerns about managing invoices and payments in QBO. You can drop a comment below, and I'll gladly help. Take care, and I wish you continued success, @francesb.