I am assuming you have already integrated QuickBooks Payroll for your business.
On the QuickBooks home page, click Liabilities
Use this window to process your liabilities payment in QuickBooks.
Click Pay Liabilities
Select the date range for the payroll liabilities you want to pay and click OK
Select the current account from the drop down menu, liabilities you want to pay, payment date and enter the amount you want to pay for each of these payroll items under 'Amt to Pay'.
Click Review at the Top Right corner of your window.
Review your cheque and click save and close.
Use this steps to learn how to pay payroll liabilities balance in QuickBooks