Answer
Lightning Payroll lets you request that more PAYG withholding be taken from an employee's pay than the standard tables require. There are two mechanisms: an Upwards Variation (the employee lodges NAT 3093 with the ATO and you record the varied amount or rate) and a Manual variation of PAYG withholding / Voluntary Agreement (used for contractors who hold an ABN; requires NAT 2772).
In the desktop app
- Open the Employees tab and select the employee.
- Click Tax Rates to open the employee's tax rate settings.
- Select the Tax Settings tab.
- To add an upwards variation, tick Upwards variation and then choose a method: a set amount per pay, a minimum withholding percentage of gross, an increase as a percentage of calculated tax, or an increase as a percentage of gross.
- To set up a Voluntary Agreement instead, tick Manual variation of PAYG withholding / Voluntary Agreement and enter the payee's ABN.
- Save the employee record.
In the online (web/mobile) app
- Go to Employees and select the employee.
- Open the Tax section, then choose Tax Settings.
- Make sure System Generated Tax Rate? is ticked (this is the default). The Upwards Variation checkbox will then be visible.
- Tick Upwards Variation and choose either As a set dollar amount per pay or As a percentage of tax, then enter the value.
- To use a Voluntary Agreement instead, tick Manual variation of PAYG withholding / Voluntary Agreement, enter the withholding percentage, and provide the payee's ABN.
- Click Save Changes.

For information on setting up a Voluntary Agreement for a contractor, see How Do I Set Up Voluntary Agreements in Lightning Payroll?