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Single touch payroll has been brought in for all businesses now (I believe?) so if you haven’t set up, go through Xero and this will connect you direct to ATO.
Then when you record the pay run, you will file it and the information goes directly to the ATO.
At each BAS period (pending if you are quarterly or otherwise), you’ll complete the BAS and record the PAYG withheld and gst … and pay ATO whatever the required payment.