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Hi natewang,
If you've already processed pay runs with paid dates on or after 30/3/20 but are wanting to claim JobKeeper payments for these pay runs, you will need to notify the ATO and pay your employees the Top-Up amounts. You can do this either by recording these in a new payrun or amending the previous and lodging an Update Event.
This article will guide you through the steps to report the JobKeeper Start fortnight and and record the Top-Up amounts for each eligible employee. If you've used the employees 'normal' pay category for their earnings to date and now need to change this to the Top-Up category, see the section 'I've already paid employees through JobKeeper a different way' for steps to correct this.
The JobKeeper Start category is used to notify the ATO when you're claiming the subsidy from; it is based on the first time you paid your employees JobKeeper, and it's the name on the pay category that's informing the ATO, not the pay period it's reported in. So if you are creating a new payrun rather than amending existing, you can enter the category there; 'You cannot forward date the fortnight start entries in the pay run, but you can add it to a subsequent pay run, if you've already started paying your eligible employees JobKeeper'.
-Kass
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