I will double check with our accountant, although typically as a CIS sub-contractor you should be invoicing the contractor the gross figure (as per the guide here), the only thing you would need to do is itemise the labour and materials part, this will allow the contractor to calculate the appropriate deduction. The deduction is something the contractor would need to calculate and report to HMRC. If the deduction is applied on the subcontractor side you would be under reporting your sales.
The subcontractor guide I linked to above also explains how to pay the invoice in full to the CIS holdings account and transfer the lower amount into the bank to align with the payment made.