Hi Cheforce
Thank you for your post.
If an employee wants super paid into multiple funds, they'll need multiple employee cards. This is because you can only assign one super fund to an employee's card. You will have to set up one primary card for their payroll information, and this card is linked to one super fund.
For additional super funds, a new employee card is needed to store the fund information. When the employee is paid, the fund linked to their primary card is paid as normal. The payments for the additional funds are temporarily held in a "clearing" account, then distributed to the other employee cards and their associated super funds.
I've attached a reference article that is for our AccountRight product range but will give you an idea of how it works: Employees with multiple super funds
In terms of STP reporting, it would be best to check with ATO on how they will accept the information from two different cards.
Please feel free to post again. I'm happy to assist further.
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