engine.io is a lower level library than socket.io.
Engine is to Socket.IO what Connect is to Express.
If you want the lower level abstraction, use engine.io. If you want a websocket abstraction, keep using socket.io.
engine.io is of more interest to you if you’re building a library/framework on top of socket.io.
socket.io is of more interest to you if you’re building an application on top of socket.io.