Let me guide you on how to fix your employee's pay run. You can unlock the pay run and enter the necessary adjustment on it. Here's how:
Go to Employees tab.
Select Pay Runs and then select the pay run you wish to unlock.
Select Pay Run Actions then choose the Unlock.
Enter in a Comment about why you’re unlocking the pay run then select Unlock.
Once done, you can adjust the net pay of the employee by clicking on the drop-down menu of employee's name to expand the details of it. Then on Actions drop-down menu select Adjust PAYG. If the amounts on the pay run are correct, you can refinalise it.
Here's how to create and lodge an update event:
On Employees tab select Reports.
Select Single Touch Payroll.
Select the Create Update Event button.
Select the appropriate Financial Year and Pay Schedule, then select Create. It will show you the list of all employees related to that pay schedule along with their year-to-date payroll details.