Sub Contractor with Schedular Payment and GST

[Samiauto]

Hello,

I have set up a contractor in payroll who I pay witholding tax. Unfortunately, he is now also GST registered. From another post I set up a pay item in payroll for him that accounts for the GST portion of his invoices. I think this part is all going well. 

However, I am struggling with what I should be coding the journal to account for the GST. I thought it was all going well. I credit the Wages and Salaries account and debit the GST Paid. It all appears to be debiting and crediting the right accounts when i look at general ledgers for the specific accounts, but now I have gone to do my GST return the sub contractors GST Paid is not showing up as it is showing in the exempt section. I feel I am doing something blatantly, obviously wrong but I can't seem to fix it.

Thanks Sam