As per HMRC's guidance, businesses that are on Cash VAT scheme will be able to use the CIS RC as long as the invoices are accounted for on a Standard (accrual) VAT scheme.
QuickBooks accounts for your transactions on a Standard scheme when using the CIS RC. Go to the section "Where can I find the codes and how do I activate them?" to turn them on.
If you are on the Cash VAT scheme, your VAT return (VAT 100) will show correctly accounting for your transactions on an Accrual basis. We are working on having the VAT detail report reflect this and will be coming soon.
To verify the amounts on the return, run the VAT liability report for the VAT period on cash and accrual, make a note of the RC CIS sales amount (box 6) and/or RC CIS purchases amount (net amount for box 7, tax amount for boxes 1 and 4) for both methods.
Take the detail report total for the required box and deduct the cash-based RC CIS amount from the liability report, then add on the accrual-based RC CIS amount. This will give a figure that matches the prepare return and VAT 100 figures.
To see the accrual transactions, you can drill into the RC CIS amount on the accrual liability report.