Both rules apply to the same payment and do not interfere with each other. CIS decides how much you keep back for HMRC. The reverse charge decides who accounts for the VAT.
| Invoice, excluding VAT | £5,000 |
|---|---|
| Less what the subcontractor paid for | £1,500 |
| The rate applies to | £3,500 |
| CIS deduction at 20% | £700 |
| VAT on the invoice | £0 |
| Pay the subcontractor | £4,300 |
| VAT you account for under the reverse charge | £1,000 |
Whether the reverse charge applies at all depends on who your customer is and what the work is. Check that first.