Yes, the engines are currently just in transparent testing - running parallel to the existing engine code. As it is still not able to replace all capabilities of the existing code, I decided to include it like that. When the ATVC code is there and we can route the existing GPC commands to it, we can make comparative testing and finally switch simply over to your code - and back if something goes wrong during runtime which we can mitigate.
The creation of the engines inside Realize() will have to change. I know it was my idea, but I more and more notice, that the responsibility for all directly Orbiter related resources belong to the Atlantis class - meshes, propellant resources, attachments, docking ports, light beacons and thrusters.
As such, I think the better way to implement the SSMEs for you will be:
The Atlantis class creates them and makes them available for the SSME objects over a public interface. When they are not available(for example during initial creation, but also later for testing), the functions give you a error condition which means you are operating in transparent mode.
You can still use the functions as usual in transparent mode, but they will not have effect.