Hi 

I ended up creating a new P&L code for CIS materials, just as a COS account with COS as the detail type.

I removed the supplier as a sub-contractor and left them as a normal supplier. 

This only helps with the P&L code though so you can track the purchases without the supplier needing to be marked as a sub-contractor. 

At the moment our company is the sub-contractor and we don't have any sub-contractors, therefore QB thinks we're not fully set up for CIS so I'm still not able to submit the deductions to HMRC through QB. I've had to download the HMRC tools to submit the EPS through that. 

It seems the P&L codes set up by QB for CIS are all set to 'With-holding tax purchase' as the detail type, but this seems irrelevant because it's only the CIS suffered that a contractor or sub-contractor would be claiming back from HMRC and the purchases are tracked so that you have the information available for when you hit the threshold for applying for gross payment status. 

Sorry that's not much help, but hopefully the developers will change the set-up because it won't work for anyone the way it is at the moment!