Here’s how you can set up a payroll account in QuickBooks. 1. Get an employer identification number. 2. Check whether you need state/local IDs. 3. Know the difference between an employee and an independent contractor. 4. Give attention to the employee’s paperwork. 5. Decide on a pay period. 6. Document employee compensation terms.  7. Choose the payroll method. 8. Run payroll. 9. Record the payroll service. 10. Report the payroll taxes.