If you are using the same QB to run payroll and pay taxes, the accounts should be adjusted accordingly. I think the confusion you are having is what is an expense and what is a liability. Remember, the bulk of your tax payments are from the employee and have already been expensed as payroll. That is why these amounts are held in liability account until the payments clear them. But, every employer has additional taxes as they match FICA. Additionally, there are other 'taxes' like UI that cost the employer amounts over the gross payroll. These are typically added as an expense to the payroll tax account. Some just include these amounts in the general payroll expense account along with wages, but I prefer to break it out to 'Payroll:Wages' which is gross payroll, and 'Payroll:Taxes' which are additional amounts paid by the employer (Not withheld from paycheck). As with most items in QB the setup is based on the preferences of you and/or your bookkeeper.
