If you have an employee who is tax-exempt or on a researcher tax scheme, you can specify it during step 3 when adding the employee.
To enable the setting go to Company -> Advanced -> Enable More income types:
When creating a new employee it is possible to change the income type. Under Income type -> Choose either Researcher arrangement or Taxfree income:
Please note that Salary cannot confirm nor verify whether an employee is eligible for a different income type than 00, which is standard. Therefore, we recommend that you consult with your accountant when it comes to researcher tax schemes and tax exemptions.