AutoEntry does not automatically process CIS payments, but they can be entered manually. This article will take you through the steps!
The totals will require editing in the header (examples below being from one invoice):
The net is edited to the net figure minus the CIS payment. Tax is as extracted by AutoEntry, and the total is edited to the total minus the CIS payment.
Then 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.
Net/VAT/Total then match the header and the invoice can be published.
Xero has launched a beta version of a CIS module which they have not made accessible yet to apps publishing invoices to Xero. If the CIS module is turned on, for the beta version anyway, you cannot publish invoices from AutoEntry to those CIS specific category accounts.