AutoEntry does not automatically process CIS payments, but they can be entered manually.
How do I create a CIS payment on an invoice?
The totals can be edited in the main body of the invoice. The Net amount should be edited to 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, and the second line for the CIS payment in the negative.
The Net, VAT and Total amounts should then match, and the invoice can be published!