The effects of flow alignment on the relaxation dynamics of a lamellar diblock copolymer melt and the dynamics of flow alignment itself are investigated using simultaneous measurements of shear stress and birefringence in both the flow plane and the sample plane. The primary advantage of this rheo-optical approach in the context of flow alignment is that it provides quantitative measurements of the evolution of the macroscopic mechanical properties and the state of the microstructure in real time, in situ as alignment occurs. Further, it provides information on the molecular and microstructural dynamics that give rise to flow alignment. An entangled, nearly symmetric poly(ethylene-propylene)-poly(ethylethylene) of 50 kg/mol (PEP-PEE-2) is studied during flow alignment under two different conditions, one that enhances alignment of the lamellae parallel to the sample plane and another that induces alignment perpendicular to the sample plane (lamellar normal along the vorticity axis). The results suggest that the flow process leading to parallel alignment PEP-PEE-2 is associated with inhomogeneous deformation such that the orientation of domains in the material undergoes irreversible "rocking", while the process that produces perpendicular alignment occurs under conditions in which the deformation is nearly homogeneous throughout the material.