See more information about pay categories: Pay Categories - Creating & Managing.

If you are paying this employee specifically for jury duty leave, you need to set up a pay category for it. You might not be sure how you should classify the payment category, Reference guide for STP Phase 2 pay category payment classifications.

No superannuation is required as per this article: https://www.ato.gov.au/businesses-and-organisations/super-for-employers/paying-super-contributions/how-much-super-to-pay/list-of-payments-that-are-ordinary-time-earnings

Jury duty does have a classification in the article:

See more information about managing leave categories: Managing Leave Categories.

Once the payment category is created, you can then create the leave category (if you do not want to use the paid Community Service Leave). (If you were not paying the employee for the period they were on leave for jury duty, you would only need to create the leave category.)  Ensure that you select the correct pay category that you have created for the leave category.

Tick the Jury Leave Category on the relevant Leave Allowance Templates so that employees can apply for the leave.

See more information about setting up deductions: Setting up Deductions.

To deduct the amount already paid to the employee, you can create a post-tax deduction category (employee was paid the $40 post-tax by the government.

Then in the pay run you can apply the leave to the pay run and then deduct the amount using the newly created deduction category by selecting Actions > Make a Deduction.