In this work, we present a general route to hybrid quantum mechanics/molecular mechanics dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the polarizable force field AMOEBA to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions.We discuss in details the implementation and demonstrate the global energy conservation using density functional theory. Finally, the approach is assessed on the electronic absorption properties of an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent density functional theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.