If you see a payment in red on the Pay Taxes page, it's overdue. You can make late payments to the IRS. For state taxes, some will block you. You may need to contact the state to make the payment. Then, In QuickBooks Online, you can manually record it as prior tax history.
Let me show you how:
Go to the Taxes menu and select Payroll Tax.
Under the Taxes section, click Enter prior tax history.
Click Add Payment.
Enter and select the correct details.
You can review your tax liability report to see if it was successfully posted.
Feel free to visit these pages for more details in handling payroll taxes: