Yes. To route an order to IBKRATS via the API, you need to set the IBApi::Contract::Exchange field to "IBKRATS" and IBApi::Order::NotHeld to True.
Note: The order must have the NotHeld field set to True, or you may receive a rejection with the reason: "IBKRATS order must be a not-held". When IBKR ATS orders are submitted via TWS, this field is set automatically.
Find out more in the TWS API Users' Guide.