Simple answer: "You don't"
You can affect the object directly once you have become one with it (feel it in you).
Sometimes it has seemed as if the mind tunes in to the resonant frequency of the target and then locks in a standing wave or something. Depending on the concentration, sometimes I have acquired a connection with other objects surrounding the target.
However, I think one could also do it with wind as well. But even in this case, you wouldn't focus on displacing the atoms. You would just become one with the air and move. I don't think micro-management is needed.