Voucher Match for landed cost invoices from clearing agents

Our users are reviewing the possibility of using voucher match for landed cost invoices from clearing agents. As per our new setup, system creates GRN for clearing agents and user can go and select record during voucher match. But the problem they face is; the total invoice amount in the clearing agent’s invoices is not always same as the accrued amounts during GRN. How can they handle the variance amount? Some invoices need over payment, some needs under payments.  

Thanks and kind regards,