Hi there, @calicoellie.

Thanks for posting your concern in the Community space. I can help you correct the payroll with undeleted bonus and paid payroll taxes.

It's best to create a payroll liability adjustment since you already paid the taxes for the check which included the extra bonus to be deleted. 

Here's how:

1. Go to Employees menu.
2. Select Payroll Taxes and Liabilities.
3. Click Adjust Payroll Liabilities.
4. Supply Date and Effective Date.
5. Choose between Company and Employee adjustment.
6. In the Taxes and Liabilities table, enter all necessary information.
7. Then, click the Accounts Affected button to select where this adjustment will affect.
8. Click OK.
9. In the adjustment window, click OK to save adjustment.

For more information and reminders in creating a payroll liability adjustment, just refer to this article: https://community.intuit.com/articles/1762814.

To check taxes being withheld, you may pull up the Payroll Summary Report.

Once done, taxes will show up on the form for the next filing an overpaid amount. You'll have the option to ask refund from the government or apply the credit to the next return.

This information should correct your taxes and payroll in QuickBooks. Keep me posted on this by leaving a comment below. I'll be around if you have other questions. Have a nice day!