You can create after tax additions for allowances that are not reported to the ATO via STP Reporting. You will need to select an STP reporting group for before tax additions.
The example below is an amount based allowance, e.g. travel allowance or reimbursement, where you need to pay the employee an amount.
Go to Payroll, Maintenance, General, Additions and Deductions.
Click Add.
Enter the Code, Shortcut Key and Description.
Select Additions After Tax as the Category.
Select the Type as Amount.
Click STP Reporting, leave the STP Phase 1 options as default, as you are now reporting to the ATO using STP Phase 2.
For STP Phase 2 select Exclude from STP Reporting for the Reporting Group.
Click OK.
Once the new addition is created, attach it to the employee's record if it is part of their standard additions and deductions. If not, you can use this code when you enter timesheets.