Manager has not included compulsory superannuation for me in the past. The ATO requirements and definition of W1 in Manager are listed in this thread Aust localisation inconsistent with ATO requirements
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It should include almost all in payslip earning
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Not be effected by payslip Deductions (such as salary sacrifice) and Contributions
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Note your employee pay is decreased by salary sacrifice but W1 is not as it reports Gross pay
What version of Manager are you using?