Thanks for reaching out the Community support, @ABH89.
Let’s get this straightened out for you.
You’re on the right track in correcting those paid payroll liabilities written in Write Checks. Creating a negative amount that is equal to the liability checks zeroes out the check amount.
In addition, penalties are not part of the Payroll Liabilities and should be tag under Expenses when creating a liability payment in QuickBooks Desktop.
I’ve got you an article on how to handle liability payments made in Write Checks: Correct liability payments made in Write Checks instead of Pay Liabilities.
Keep in touch if you have additional questions while correcting liability checks. I’d be glad to answer them for you.