You are on the right track here, just need a little light shed on the process. 

When you run your payroll, QBO will debit the payroll tax expense and credit the liability. This records your expense when you are incurring it rather than waiting until you pay it. When you are ready to pay the taxes, you will debit the related liability account and credit your cash account. So when you pay your Federal 941 taxes you should debit the Payroll Liabilities - Federal 941.