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If your employee works during a jobkeeper fortnight, even for an hour, they need to be paid $1,500 to cover the full fortnight. As you should also be processing unused leave this is also included in the fortnights pay. So if salary is $700 for example and they have $1,000 in unused leave, there is no top up due as total received is above $1,500 threshold for the fortnight.
If pay plus unused leave and other termination payments is less than $1,500 then you have to make the top up payment.
Hope this helps.
I think this Link should assist:
From reading 3rd paragraph down (Copied below) you should still get the $1,500 per fortnight upto to 27 September providing that both you and your employer meet all eligible criteria.
If you are stood down or have reduced hours
If you normally earn more than $1,500 but are stood down or working reduced hours, such that your ordinary income is nil (that is, stood down) or less than $1,500 (that is, reduced hours) per fortnight before tax, then your employer must pay you at least $1,500 (before tax) per fortnight in order to receive the JobKeeper payment.
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