We’ll look at producing a guide to this shortly.
It would almost be a mirror to this guide. You would record the full invoice value otherwise your income figures would be lower than what they actually are. The company you invoice (the contractor), would just pay 20-30% lower than what’s been invoiced (this depends on their registration with HMRC (see this guide).
For example, we invoice for £500.00, they pay 80% - £400.00.
Then, as per the guide I linked to above, you would have a dummy CIS bank account that you would tag the invoice as paid in full to.
When the money actually arrived (the £400), you would tag it as a transfer to the CIS account, essentially making your CIS account -£100.
Note: I’m not an accountant