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Photoinduced electronic energy transfer in conjugated donor-acceptor systems is naturally accompanied by intramolecular vibrational energy redistributions accepting an excess of electronic energy. Herein, we simulate these processes in a covalently linked donor-acceptor molecular dyad system by using nonadiabatic excited state molecular dynamics simulations. We analyze different complementary criteria to systematically identify the subset of vibrational normal modes that actively participate on the donor → acceptor (S2 → S1) electronic relaxation. We analyze energy transfer coordinates in terms of state-specific normal modes defined according to the different potential energy surfaces (PESs) involved. On one hand, we identify those vibrations that contribute the most to the direction of the main driving force on the nuclei during electronic transitions, represented by the non-adiabatic derivative coupling vector between donor and acceptor electronic states. On the other hand, we monitor normal mode transient accumulations of excess energy and their intramolecular energy redistribution fluxes. We observe that the subset of active modes varies according to the PES on which they belong and these modes experience the most significant rearrangements and mixing. Whereas the nuclear motions that promote donor → acceptor energy funneling can be localized mainly on one or two normal modes of the S2 state, they become spread out across multiple normal modes of the S1 state following the energy transfer event.