Hi nicshort30
If you are creating an invoice in relation to CIS, you are the subcontractor and you are sending it to the contractor, you then receive payment on the invoice, the amount will show in the Income section of the P&L.
If you are creating an expense n relation to CIS, you are the contractor and your supplier is a subcontractor, you have received their bill and made payment, this is a cost to you and will appear in the Cost of Sales section of the P&L