Xero have launched a new feature to handle CIS payments, currently in Beta testing (available for use but not the completed program). It is currently not possible to post invoices from AutoEntry to the CIS specific accounts/module. Xero has not added this feature to the API that allows us to do so (no external app has access).
Xero does not at this time have a time-frame on when or even if this feature will become available. We do have a workaround to post CIS invoices avoiding the new CIS specific accounts that Xero use, here.
From Xero - "Currently it's not possible to use the Xero API or other third party apps to import CIS bills or invoices into Xero."