A method and system for controlling an engine includes a spark ignition (SI) control module operating the engine in a spark ignition mode in a high lift valve state and a pre-HCCI control module entering a matching state when homogeneous charge compression ignition (HCCI) mode conditions are met. When a matching condition is met, the pre-HCCI control module enters a pre-homogeneous charge compression ignition mode and performs spark retardation, stratified operation or lean operation and commands a low lift valve state. The system also includes an HCCI control module entering an HCCI mode and when in the low lift valve state.