How to perform a Prepayment on a Work Confirmation with 3-way match

The Engineering department typically pre-pays suppliers for material stored on site and then applies the prepayment to later invoices. However, we're not sure how to prepay when using a work confirmation that requires a 3-way match. There is a 'material stored on site' field on the work confirmation, but it is treated like a normal receipt and not like a prepayement. 

Thanks,