Before paying an employee for the first time under Auto Enrolment, you should ensure that you have configured all of your additions and deductions, flagging which of these payments should be used when assessing whether an employee should be automatically enrolled into an Auto Enrolment Scheme.
To do this navigate to Company > Additions and Deductions.
In this screen highlight the addition that you want to count towards Qualifying Earnings and tick the QE checkbox.
For more information on Qualifying Earnings, go to The Pensions Regulator’s webpage on Assessing the Workforce.