Hi Bernieozz
Thanks for your post. Each pay run is a separate transaction, so one won't override the other. There are some situations, like bonus payments and adjustments, where you will need to record multiple pay runs for the same pay period.
If a pay transaction is incorrect you need to reverse that pay transaction to fix the YTD amounts in the software. This will also update the YTD amounts in STP. The Help Article, Changing a recorded pay, has more information.
Please let me know if you need further help.
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