AutoEntry doesn't automatically process CIS payments, but you can enter them manually.
How do I create a CIS payment on an invoice?
You can edit the totals to be edited in the main body of the invoice.
You should edit the Net amount to be the Net figure minus the CIS payment amount. The Tax amount remains extracted by AutoEntry, and the Total amount is edited to the Total minus the CIS payment.
Manually add 2 Line Items (not Tax Summary).
One line for the total value of the invoice excluding any CIS payments
The second line for the CIS payment in the negative
The Net, VAT and Total amounts should then match, and you can publish the invoice.