Hiya @emhauv
Your employer just deducts the additional PAYG withholding and pays it to the ATO as a single amount. When they report your income, PAYGW and super guarantee to the ATO through Single Touch Payroll, there's just a single figure for tax (PAYGW).
Here's some great guidance from the ATO that may better demonstrate how it works. "Reportable super contributions" reflects your salary sacrifice to superannuation.
I hope that helps - Deanne
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