You are able to process a NIL pay by adding 0.00001 as the pay (gets processed as a nil pay) and having the superannuation salary sacrifice amount recorded and allocated to the super liability account. Double check that the SS amount appears in the RESC box on the PAYG Certificate. Also make sure the employee has provided the employer with a letter / statement requesting the 'pay' to be 100% salary sacrificed
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You may also find this PDF document useful. It says for QuickBooks 2009-10 but it still applies for any version above this.
Hope this helps.
Luke.