When the Super Allowance percent has a value, if an employee does not reach the threshold value set in the Super threshold field for the month, then following month they will receive a Payment in lieu of super under their Gross allowances (when the first payroll for the month is processed).

The super allowance is shown as follows within the payroll 

Example: in this example, the employee earned $314.16 in the previous month, so the allowance of $15.71 given in the next payroll month represents $314.16 x 5%.