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Simultaneous rheological, polarized light imaging, and small-angle X-ray scattering experiments (Rheo-PLI-SAXS) are developed, thereby providing unprecedented level of insight into the multiscale orientation of hierarchical systems in simple shear. Notably, it is observed that mesoscale alignment in the flow direction does not develop simultaneously across nano-micro lengthscales in sheared suspensions of rod-like chiral-nematic (meso) phase forming cellulose nanocrystals. Rather, with increasing shear rate, orientation is observed first at mesoscale and then extends to the nanoscale, with influencing factors being the aggregation state of the hierarchy and concentration. In biphasic systems, where an isotropic phase co-exists with self-assembled liquid crystalline mesophase domains, the onset of mesodomain alignment towards the flow direction can occur at shear rates nearing one decade before a progressive increase in preferential orientation at nanoscale is detected. If physical confinement prevents the full formation of a cholesteric phase, mesoscale orientation occurs in shear rate ranges that correspond to de-structuring at nanoscale. Interestingly, nano- and mesoscale orientations appear to converge only for biphasic suspensions with primary nanoparticles predominantly made up of individual crystallites and in a high-aspect ratio nematic-forming thin-wall nanotube system. The nano-micro orientation propagation is attributed to differences in the elongation and breakage of mesophase domains.