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Hi eventswest,
I would encourage you to read over this helpful Managing JobKeeper Payments guide which is updated to confirm the new JobKeeper outlines. It's extremely helpful in ensuring your payroll system is set up to be included in the extension.
To answer your concerns, based on JobKeeper 2.0 way of Processing JobKeeper Payments it does encourage you to use the system generated option to be sure the figures are reported correctly. You may need to consider moving forward, even if the ATO is satisfied with your previous payments, during the new scheme to use this Add JobKeeper Payment Option.
For any assistance with this process or if you have any further followup questions related to a company file, please don't hesitate to reach out to us by clicking here.
Thanks,
-Steven
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