Payroll Service or Payroll Software – What is the Real Difference? This is why most of the businesses reach for the help of the payroll services from specialized agencies, while the other reach for the payroll software as the right solution for their payrolls. A good accountant or good payroll software, it is up to you to decide what is more reliable. Payroll software comes with a fee that is not really comparable to the payroll service. When you opt for payroll software, then things get much easier and better.