The interface of the physical and the spiritual

Those who believe in a spiritual world where god and the human soul reside presumably have in mind some process by which this world interacts with the physical world where our bodies exist and where we apply scientific method.  

When we have discussed free will it is clear that believers envisage the soul as the vehicle for exercising free will. Presumably physical brain activity plays some part in our behaviour but how does the soul exert control? How does the soul contend with physical influences such as brain damage, drugs and electro stimulation?

Similarly god acts upon the world. How does he influence physical processes? Again presumably the spirit world can presumably override the usual physical laws. In order to accomplish miracles god would have to subvert simple conservation laws and generate measurable energy. How does this mechanism work? Obviously I don't expect believers to be able to explain the ineffable workings of god in detail but the spirit world is not detectable by physical means and yet it can change the physical, believers must have some view as to how this happens. 

The problem for me is that we have tools to investigate the physical world, these tools are not much use when it comes to the spiritual world. It seems as if the spiritual world must 'trump' the physical world in that it can subvert the usual physical laws. When this happens there must be a clear boundary that can be observed. Obviously miracles resulting from the direct intervention of god are not that common and if they are I am sure that god would not tolerate being measured. However the exercise of freewill is a daily occurrence. As neuroscience becomes more sophisticated will we be able to detect where the physical leaves off and the soul takes over?

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