Check your employee account > Payroll details and make sure that when you click the Superannuation tab that they are receiving Superannuation Guarantee payments.
You don't pay super to the ATO, just report it has been paid. The Super Contributions are paid to the employee's chosen Complying Super Fund as stipulated in the employees account details.
They need to supply you with their chosen CSF Member number when they started employment with your company, which should be included in their employment details tab. Once correctly entered, the superannuation payment will be shown in the Payroll run a copy of which is sent to the ATO under the new Single Touch Payroll provisions.