If you have made a payment by EFT and you need to modify the return amount you can do the following:
If you require a full/partial refund of a return payment, contact Payroll Tax at payrolltax@sa.gov.au
If you need to make an additional payment, you can submit a further return for the period for the additional payment amount by completing the following steps.
To generate a further EFT advice, click on the Generate/View EFT Payment Advice link in the Action column of the desired return.

The Generate EFT Payment Advice screen is displayed. The previously entered EFT expected payment details are displayed in the bottom portion of the screen.

Enter the additional amounts and override the deduction entitlement to zero if you have already claimed the full deduction on your first advice. Click on Calculate and RevNet will automatically calculate the Tax Payable figure.
Select Generate EFT Advice and you will receive a warning message reminding you that you have previously calculated an amount payable and that this new amount is in addition to the previous payment/s.
The EFT Payment Advice screen is displayed.
Select Print to print this
page and then use the information to make your EFT Payment through
your financial institution.
Please Note: The BSB,
Account Number and Payment
Reference Number must be all correctly included with your EFT
payment.