Nice to meet you, @jake2210. Thank you for joining the thread and for sharing with us your concern about managing customer overpayment in QuickBooks Online (QBO).

We can share some information and steps on how we can record the customer overpayment that has deposited with another invoice. Let's create a check or an expense to record the refund for your customer.

Here's how:

1. Click the +New, then select Expense, Add Expense, or Check.
2. Fill out the needed details.
3. Select the bank account to which you deposited the overpayment from the Payment Account dropdown.
4. In the first line of the Category column, select Accounts Receivable.
5. Enter how much you want to refund in the Amount field.
6. Once done, click Save and close.

Afterward, you can link the refund to the customer's credit or overpayment. Check this article for the detailed steps: Refund a customer's overpayment or credit.

We'll also include this article for more information about managing customer credits and refunds in QBO:

• Record a customer refund in QuickBooks Online
• Void or refund customer payments in QuickBooks Online
• Handle a customer credit or overpayment in QuickBooks Online
• Remove or Unapply a credit from an invoice or bill

@jake2210, please get back to the thread if you have clarification about the process of recording a refund. We'll always be happy to help you. Have a great day ahead and a prosperous business!