The following section of the HMRC guidance may help here (src):
How to make a CIS deduction
To make a deduction from a subcontractor’s payment, start with the total (gross) amount of the subcontractor’s invoice.
Take away any of the following the subcontractor has charged for:
- equipment which is now unusable (‘consumable stores’)
- fuel used, except for travelling
- equipment hired for this job (‘plant hire’)
- manufacturing or prefabricating materials
- Finally, deduct the CIS percentage rate (as given to you by HMRC) from the amount left. You’ll be left with the net - amount you need to pay the subcontractor.
Whatever CIS you deduct will determine the NET amount you pay to the subcontractor and the figure transferred from your current account to the CIS holding account.
The example in the guide uses £500 gross and £400 payable, but it could easily be £500 gross and £350 payable.
If you have any doubts I’d recommend running it by your accountant just to be sure.