Use W-4 Amounts

I have an employee who thinks not enough is getting taken out for Federal Withholding.  Right now he has Filing Status of Married, 0 exemptions.  I have the 'Use W-4' box checked because that is what I was always told to do.  I tested a payroll run and unmarked that 'Use W-4 box' and now more Federal Withholding is being taken out.  What is the point of the Use W-4 box if there are no other exemptions being held?