Jones,
I was hoping to get a material document generated with the info from the scrap qty field
If I understand your question correctly if you want to generate a material document with yield,scrap during order confirmation then you should have auto GR for header and Auto back flush for components.
Auto GR can be set at Production scheduling profile which is assigned to your header material in work scheduling view or Through the Routing operation control key.
Auto back flush for component you can set at Material master or in Work center or in Routing.
after above changes test the scenario again and see if that works.
BR
KK