Marlin GTX enables automated superannuation payment compliance using the Payday Assist integration.
New ATO Payday Super rules take effect from 1 July 2026.
These rules require all Australian employers to pay super at the same time as wages, with contributions required to reach employees' funds within 7 business days.
To support this, the new Payday Super Assist integration can automatically handle your super payments through the SuperChoice clearing house each time you submit a pay run.
For more information, or to enable the Payday Super Assist integration in your HR system, please contact your account manager.
If you decide not to use the Payday Super Assist integration, you will need to set up and manage your own clearing house.
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Setting Up Payday Assist
How do I set up the Payday Assist integration?
Instructions about how to enable the Payday Super integration and set up your SuperChoice account will be provided once it has been approved for your account.
Once the SuperChoice integration is approved, you will need to:
- Update to HR version 5.4.8 or later
- Verify all employee and super fund information is complete and correct in HR
- Register and set up your account with SuperChoice
- Go to www.employerpay.com.au/EmployerPortal/register/custodian/megabus and follow the provided Employer Self Enrolment user guide
Searching for SuperChoice in your browser takes you to the generic site, not the Megabus SuperChoice portal.
If you cannot log in to the SuperChoice portal after registering, you may be using the wrong URL.
To access the correct Megabus portal:
- Use the http://www.employerpay.com.au/megabus
- Or click View in your SuperChoice registration welcome email
You can also save the URL in your bookmarks for future use.
- After registering with SuperChoice:
- Enable Payday Super Assist integration in HR
(following the provided Payday Super Assist Set Up guide) - Warning: If the integration is enabled before registering with SuperChoice, your pay runs will send files to SuperChoice which will be rejected
- Enable Payday Super Assist integration in HR
Megabus recommends using your primary payroll email address as the user name when signing up to SuperChoice (step 9).
Changing to SuperChoice
How do I change to the SuperChoice clearing house?
If you decide to use the Payday Super Assist integration, you will need to go to www.employerpay.com.au/EmployerPortal/register/custodian/megabus and follow the provided Employer Self Enrolment user guide to enrol your business.
When to Change Clearing Houses
When should I change clearing houses?
If you are using the Payday Super Assist integration, you should switch over to SuperChoice immediately.
You must also set up the Payday Super integration with SuperChoice before commencing the first pay run for the new financial year, so that the super payment file can be automatically submitted.
When to Enable Payday Assist
Do we enable the Payday Assist integration in HR before or after final pay run of the financial year?
It is up to you whether you want to start using SuperChoice and the Payday Assist integration.
You can continue to use your old clearing house/method to process payments prior to June 30 (see below).
However, if you are using Payday Super Assist, it must be enabled for the first pay run of the new financial year.
First Pay Run
Do we need to set up the SuperChoice pay period as 01/07/26 or as our next pay run day?
Employers must comply with the PayDaySuper rules from the first pay run being paid on or after July 1 2026.
However, you can complete the set up instructions we have provided earlier than this and commence using the SuperChoice integration earlier if you wish.
Mandatory Usage
Is the use of Payday Super Assist integration mandatory, or can I use another clearing house/method?
It is not mandatory to use the Payday Super Assist integration.
You are welcome to use alternative clearing houses or methods to meet the ATO's payday super requirements.
However, the Payday Super Integration provides an easy and automatic method for continually meeting these requirements as an HR user.
Manual Usage
I manually enter super payment details into our SuperChoice portal, can I still do it this way or will it be mandatory to use the exported file?
You can still enter your SuperStream information in the SuperChoice portal manually, if desired—just do not enable the integration in HR.
You should also sign up using the generic SuperChoice registration portal, rather than the provided Megabus link.
ATO SBSCH (Small Business Super Clearing House)
What if I was previously using the ATO SBSCH for super payments?
The ATO is permanently removing access to the SBSCH at 11:59pm on June 30.
Before then, you need to either:
- Activate the PayDay Super integration and sign up with SuperChoice
- Or, sign up with a different (manually managed) clearing house
Megabus also recommends downloading your transaction history from the SBSCH before then, since it will be required for future audits and any employee queries.
Indemnification
Are we indemnified if the super is not passed on or lost once it has left our account?
Although we don't believe there to be any indemnification as such, the ATO will consider an employer's actions and intent when reviewing missed payment deadlines.
An employer can minimise the likelihood of the ATO taking action against them by performing the following tasks in a timely manner:
- Maintaining accurate details of employees and super funds in Marlin HR
- Checking the confirmation email from SuperChoice for each pay run is successful, or addressing any issues flagged on the SuperChoice portal so that the submission can be processed
- Addressing any contribution rejections by the super funds