Non Taxable Travel Allowance in STP2

Hi there
Three Q's:
1) We have two line items in payroll for non-taxable travel allowance up to $5,000pa.
They have both been set up as Additions to Net Pay with exactly the same the tax codes - 'Allowance - cents per kilometre'
However, when we print out our Payroll Summary one appears in Gross Pay, and one appears in Additions to Net Pay.
Since changing the tax codes to 'Allowance - cents per kilometre', when we go to upload STP2, it includes the Additions to Net Pay travel allowance in the gross figure, but still shows it under the Additions to Net Pay line item.
2) How do we get both line items to sit on the Payroll Summary print out under Additions to Net pay?
3) Last year our reported figures aligned with STP as Adjusted Gross Pay. This year since STP2 began, the STP2 figures are coming up as Total Gross Pay, as though it is including salary sacrifice to super in the reportable Total Gross Pay - is this correct - is ATO now asking for every payroll item to be reported as Total Gross?
Cheers
Kim
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