The Most Common Use of Phase: Diagnosing Misalignment

Are the machine faces "in-phase" or  "out-of-phase" with one another ?

Phase is a common and reliable way to diagnose misalignment.  The procedure involves conducting an axial phase analysis around bearing faces as well as from bearing to bearing.  The point at which you find a phase shift of > 30° is typically the source of a problem (possibly not the only problem). Note in high axial vibration in the animation shown here. These components are 'angularly misaligned'. Are the faces of the machine "in-phase" or "out-of-phase" with one another ?

How would the transducers be oriented in this case ? Almost certainly 180° opposite (one pointing left and one pointing right). You will have to make an adjustment for transducer orientation.