This client is a subcontractor, therefore the tax is deducted by the contractor for whom they carry out the work for - therefore am confused as to how to account for it.
No, the tax isn't due at this point. When the client submits his tax return at the year end it is used to pay the tax owed. The client then either makes up the difference or receives a refund from HMRC. Think of it the same way as a prepayment.