...the position of the 2 objects will be the same after updating the physics engine.
well... you are not loading in the physics engine the same object that you load in youre game. For example you load a crate and asociate to this object a box from physics engine; this ones are not the same.
Installing the PhysX SDK you can see some samples and you can learn more if you want from the training programs and you can see how to implement the code for creating an physics engine.
First say to yourself what you would be; and then do what you have to do.