I appreciate you for getting back on this thread, maggie29. I'm here to walk you through handling your fee, sale, and refund in QuickBooks Online (QBO).

Beforehand, please be reminded that batched processed data will cause one (total amount of the transactions plus the fee) negative amount when uploaded to your bank feeds. It's the reason why matching them is not possible.

Going back, we can handle the invoice payments by maximizing the receive payments feature to clear off the invoice balance. Also, the refund can be recorded as a credit memo, expense, refund receipt, or check. It depends on which is more applicable to your situation.

Then, the bank fees are entered as a negative line item when generating it using the Bank deposit in QBO. It will allow you to move the payment from the Undeposited Funds account to the appropriate bank account.

Meanwhile, if you've yet to initiate the refund for the customer, you may use either a Credit memo or Refund receipt to enter it in QBO. For additional information and detailed steps, please check out this link as your reference: Record a customer refund in QuickBooks Online.

On the other hand, the steps provided by my colleague are applicable if you have not recorded the invoice payment, refund, and fees in the program yet. If you've added them already, we can directly clear the transactions from your Bank register to avoid duplicate data:

1. Go to the Gear icon and select Chart of accounts.
2. Look for or enter the bank account where you've designated those transactions on the search bar. Then, click View register.
3. Locate the invoice payment, fee, and refund.
4. Tick the checkmark column (✔) until the C icon shows up to mark it as cleared.

Moreover, excluding the transactions from your bank feeds is essential to avoid identical entries. It's a significant procedure to ensure a seamless process of generating your transactions manually in the program. The excluded data are not re-uploaded in the system.

Regarding your concern about creating a Journal entry (JE), it's used as a last resort to fix or balance your books. If you prefer using JE to deal with your situation, it's advisable to consult your accountant. This way, you're guided with an accurate accounting process.

For future reference, I'm also adding this article to help you if you need to organize your reports and choose what information will be available in its data: Customize reports in QuickBooks Online.

Please add a reply to this thread if you have follow-up questions regarding your transactions, accounts, or reports. We're always here in the Community to help you in any way.