On the last payrun of a financial year or on the first payrun of the next finacial year, you should notify the ATO you have completed all payroll transactions for each employee.
To acheave this you need to tick the "Final Payroll" box next to each employee on the STP submit form, see image below.
This also means you do not need to create a "Payment Summary" for the employee, read further details on the ATO website
Link to details on the ATO website
