Hi @Charlie19
This is months old so you've either figured it out by now - or gone mad in process
You not being VAT registered complicates things slightly & CIS without VAT is probably a use-case that QB doesn't handle very well.
Your manual calculation is spot on. You withhold 20% of the net invoice value & pay the customer the 80% plus all the VAT but QB will not be able to do that on one line (because it's expecting you to be VAT registered & so the VAT would be reclaimable).
As a workaround, you will have to enter this on two lines on the bill in QB.
Line 1 : Subcontractor CIS cost standard (20%) with a value of £416.67
Line 2 : Subcontractor VAT with a value of £83.33
The VAT (to you) is an expense so you will need to set up a new Category/Account Subcontractor VAT - or you may be able to use Subcontractor Gross or Materials as long as this won't confuse your systems (either would work from the point of nil deduction).
Hope this helps.