The existing set up is going to make the reporting at year end a nightmare if you have a high volume of contractors who invoice regularly with a mix of reportable and non reportable charges.
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My only concern with adding a box to be ticked at the time of invoice entry, is that staff/clients would not complete it consistenly during the year and then you would still end up in a mess at year end - so you would be having to choose the least worst option.
Or perhaps MYOB could be a step more sophisticated by having 1) a tick the box in the supplier card AND 2) GL codes that can be selected for the reporting. E.g. When coding an invoice, if the invoice is for Goods/Material only, then it is coded to GL Account 5-1000 or if the invoice is for Labour+Goods it is coded to another GL account 5-2000.
Then when doing the taxable reporting, the report should select contractors who are ticked in their card file AND total the only the amounts coded to GL Account 5-2000 (i.e 5-1000 can be excluded from the reporting).
Do you think this would work?