Entering and paying your 941 penalties is currently unavailable in QuickBooks Online since the system does not calculate and track this type of payment.
You can follow the suggestion below to pay your 941 penalties:
Pay the basic tax liability reported to you.
Contact the IRS for assistance in calculating the penalty and interest. (Alternatively, you can wait to receive a written IRS penalty notice in the mail.)
If you choose to record and enter this payment in QuickBooks Online, this will show as an overpayment and not a penalty payment. To know more about this process, check this out: Pay tax payment penalty or interest.
If I can be of help while working in QuickBooks Online, please let me know. I'd be more than willing to lend you a hand.