The evolution of the excited-state manifold in organic D/A aggregates (e.g., the prototypical P3HT/PCBM) is investigated through a bottom-up approach via first-principles calculations. We show how the excited-state energies, the charge transfer (CT) states, and the electron-hole density distributions are strongly influenced by the size, the orientation, and the position (i.e., on-top versus on-edge phases) of P3HT/PCBM domains. We discuss how the structural order influences the excited-state electronic structure, providing an atomistic interpretation of the photophysics of organic blends. We show how the simultaneous presence of on-top and on-edge phases does not alter the optical absorption spectrum of the blend but does affect the photophysics. Photovoltaic processes such as (i) the simultaneous charge generation obtained from hot and cold excitations, (ii) the instantaneous and delayed charge separation, and (iii) the pump-push-probe charge generation can be interpreted based on our study.