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Hi hello-linklane-c,
If this is a salary sacrifice for super, you can add this to the pay run for tracking by making a deduction and select Salary Sacrifice Super. Here's how:
If you don't see the salary sacrifice super when making a deduction, you can check your Deduction categories in the Payroll Settings. Here's how:
If you need to pay the employee for the amount you can do a bank transfer.
You can also check this link to learn more about deduction categories: Single Touch Payroll (STP) Phase 2 Hub.
Feel free to reply below if you have more questions. Have a great rest of the day!
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