To record a HECS / HELP debt there are two things to do:
1. Update the employee
To make sure the employee is identified as having a HECS/HELP debt, update the employee's extended tax details:
a. Open the "Tax" tab in the employee details form
b. Select "Study and Training" from the more drop down option
A list of training and loans schemes appear.
c. Select "High Education Scheme Payments".
Note: This information is submitted to the ATO as part of the STP payload.
2. Deducting HECS/HELP from an employee
To collect HECS debt payments, an employer will simply deduct additional PAYG withholding tax from the employee.
The ATO doesn't make a distinction for this type of withholding (the HECS repayment liability component is worked out by the ATO based on the employee's total income). An additional withholding may be added as an additional transaction line in each payment.
See information provided by the ATO: