How do I enter a refund check towards an invoice without leaving a negative/credit balance on the account?

Thanks for becoming a part of the Community, lindsay-martin-m.
 

When giving refunds to customers, if they have a positive balance, it will be reduced to a lesser amount. In the event their balance's already $0.00, refunding them will generate a negative.
 

You can create refund checks by starting with a credit memo.
 

Here's how:

1. In your top menu bar, go to Customers, then Create Credit Memos/Refunds.
2. From the Customer:Job drop-down, choose a customer.
3. Enter each item you're issuing a credit for.
4. Click Save & Close.
5. In your Available Credit window, pick Give a refund and hit OK.

The check will be filled out automatically. Next, you'll need to link it with your client's overpayment.

After finishing, if your customer's balance doesn't look right, you'll want to get in touch with your accounting professional for ways to resolve it. In the event you don't have one, there's an awesome tool on our website called Find an Accountant. Every ProAdvisor that can be found there is QuickBooks-certified and able to provide helpful insights to drive your business's success.
 

Please feel welcome in sending a reply if there's any additional questions. Have a lovely day!

ZackE, thank you, that will be helpful when I'm entering a refund for a customer.  However, the issue I'm having is for a vendor.  We overpaid and they sent us a refund check.

Thanks for getting back to us here, @lindsay-martin-m.

I'll share with you the steps on how to record a vendor refund. You'll need to record a deposit of the check, create a bill credit, and then link the deposit to the bill credit. Let me walk you through how.

1. Record a Deposit of the vendor check:
   1. Go to the Banking menu, then select Make Deposits.
   2. If the Payments to Deposit window appears, tick OK.
   3. In the Make Deposits window, pick the Received from drop-down and choose the vendor who sent you the refund.
   4. In the From Account drop-down, take the appropriate Accounts Payable account.
   5. In the Amount column, enter the actual amount of the Vendor check. (Optional) Enter a memo, check number, payment method, and class.
   6. Click Save & Close.
2. Record a Bill Credit for the refunded amount:
   1. From the Vendors menu, select Enter Bills.
   2. Tick the Credit radio button to account for the return of goods.
   3. Enter the Vendor name.
   4. Tap the Expenses tab and enter the Accounts on the original bill.
   5. In the Amount column, enter the appropriate amount for each Account (the amounts may have to be prorated).
   6. Click Save and Close.
3. Link the deposit to the Bill Credit:
   1. From the Vendors menu, pick Pay Bills.
   2. Check the Deposit that matches the Vendor check amount.
   3. Tick Set Credits and apply the Bill Credit you created earlier then hit Done.
   4. Click Pay Selected Bills, then Done.

Want to learn more about vendor refund? Check this article for the details: Record a vendor refund in QuickBooks Desktop.

In case you need help with other task in QBDT, You can browse a specific topic here and look for one that suits your needs. 

Let me know if you still have questions or concerns. I'm always here to help. Take care and have a great day ahead.

I'm stuck at # 3, linking the deposit to the bill.  When I go in to "pay bill", the deposit isn't there, only accounts payable (bills).  And since I can't link them, it shows as a credit on their account, which I don't want.

I'm stuck @ # 3, linking the deposit to the credit.  I go to Vendors, Pay Bills, but there's no deposit showing to select.

Allow me to step in and ensure you're able to enter a refund check to a vendor, lindsay-martin-m.

You need to make sure you're using Accounts Payable as the posting account on your deposit. See the attached screenshot below for your visual guide.

Once done, go back to the Pay Bills screen, find the deposit and mark it. Then, click Set Credits.

On the Apply Credits window, mark the credit, then click Done. Select Pay Selected Bills to record the refund.

You can visit again this link for instructions and detailed steps: Record a vendor refund in QuickBooks Desktop.

Stay in touch with me if you have follow-up questions. I'll be around to help you.