Payroll Categories - PAYG exempt

Hello

In relation to STP payment reports for employees that are sent ATO from MYOB, one of the payroll categories is the ‘motor vehicle allowance staff’; however the amount for this category is not captured into 'Gross Payments' in the reports, even though the ATO reporting category is selected as ‘Gross Payments’.

I exempted the PAYG for ‘motor vehicle allowance staff’ because the tax was calculated separately as a deduction as the tax is not the standard PAYG rates. However, it seems when the PAYG is exempted, the wage category is exempted from ‘gross payments’ as well; not sure if this the case. It's not shoing in the payment summaries. 

I suspect this could be because of the tax being exempt for this category. What we need is to report this category to ATO as part of 'Gross Payments' and still not be taxed as other wage categories.

Could you please advise how to achieve this?