This has been one of the common complaints against Cartesian dualism and serves to undermine it as a viable metaphysical system.  However, the implication at best entails that we must remain ignorant as to how the interaction takes place.  An "I don't know" in answer to your question would not mean that substance dualism is false, only that it is inexplicable (much like the relationship in quantum cosmology between dimensions - no one is quite sure how this happens if it does).  Though one cannot proffer a mechanism as if reconstructing a machine equipped with physical laws and objects, we do have some analogies that help us understand the relationship.  One such analogy comes from Karl Popper and Sir John Eccles' book The Self and Its Brain.

 

In there they explain that the mind (or soul) uses the body much like a piano player uses a piano.  Though the interaction here is purely physical, it's an interesting portrait of the relationship.  In terms of the possibility of such interaction, consider that our thoughts of pain are translated from certain signals from the damaged area on the body.  We go from a molecular disturbance to "Oh! I'm hurt!"  It works in reverse, too.  Consider that we think or imagine our arm lifting up and then it happens.  Again, analogously the system can work even if we are wrong about the interaction at the end of the day.

 

 

But given overriding positive reasons to prefer substance dualism above its rivals, we must defer the mechanics of this relationship as an explainable thing only via analogy.  Therefore, the concept of the body having a soul need not be threatened by this inquiry.