Currently, there is no ability to declare a Carnet Shipment in ACE eManifest. Highway carriers can simply leave the Carnet Shipment off when preparing their manifest, and have the driver verbally declare the shipment and present the Carnet document to the officer. If there are no other shipments on the truck, it is recommended that the carrier prepare an empty truck manifest so that prior notice requirements are still met. 

Automated Commercial Environment Review of Shipment Release Types: Trucks https://www.cbp.gov/trade/automated/ace-faq