If your organization processes refunds for credit card purchases, it is quite possible that you could face a scenario where a payment's "deposit" is negative.
QuickBooks does not natively support negative deposits, but you can follow the steps below to create the deposit in a way that matches your bank statements.
Workflow from QuickBooks Support:
If the total deposit is negative, create a Journal Entry to move the funds from Undeposited Funds to the bank account.
Select the Plus icon (+) at the top.
Under Others, select Journal Entry.
Enter the Date of the transaction.
On the first distribution line of the Journal Entry: Choose the Undeposited Funds account in the ACCOUNT column. Enter the amount of the deposit in the DEBITS column.
Note: This is the sum of the entire deposit, not just the sum of the refunds. You'll also want to enter this as a positive number for this step as well as step #5 below.
On the second distribution line of the Journal Entry: Choose the appropriate bank account in the ACCOUNT column. Enter the amount of the deposit in the CREDITS column.
Click Save. This will show a deduction from the bank account.
Next, group the Journal Entry with the payments to create a $0 deposit and remove the payments from Undeposited Funds.
Select the Plus icon (+) at the top, then choose Bank Deposit.
Select the payments and the Journal Entry you just created (the total should be zero).
The end result can be seen in the bank register. You will notice the zero dollar deposit alongside a journal entry showing the debit from your bank account.
When you next reconcile that bank account, you will want to include the zero dollar net entry to keep your reconciliation report clean.