AutoEntry does not automatically process CIS payments but they can be entered manually.
The totals require editing in the header (examples below being from one invoice):
Net is edited to the net figure minus the CIS payment. Tax is as extracted by AutoEntry. Total is edited to the total minus the CIS payment.
Then manually create 2 line items (not tax summery):
One line for the total value of the invoice excluding any CIS payments. The second line for the CIS payment in the negative.
Net/Vat/Total then match the header and the invoice is processed as two line items.
***Note***: 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 (as of Feb '18).