Paid sub contractor before receiving invoice, having deducted 20% CIS. Should I just input the invoice as though received before payment and then match?

Hello Lorriane10, 

Welcome to the Community page, 

Is the payment to the subcontractor in the for review sections on the banking page?

If so you can just add the CIS to the invoice you have done already and then match it up. 

If you have just manually recorded the payment you'll have to make sure it has been made to the creditors account with NO VAT to make sure it only counts for the CIS once.  

If you have any Qs please reach back out to us.