We propose an electron-phonon parameterization which reliably reproduces the geometry and harmonic frequencies of a real system. With respect to standard electron-phonon models, it adds a double-counting correction, which takes into account the lattice deformation as the system is dressed by low-energy electron-phonon processes. We show the importance of this correction by studying potassium-doped picene (K$_3$Picene), recently claimed to be a superconductor with a $T_c$ of up to 18 K. The Hamiltonian parameters are derived from ab-initio density functional theory, and the lattice model is solved by dynamical mean-field theory. Our calculations include the effects of electron-electron interactions and local electron-phonon couplings. Even with the inclusion of a strongly coupled molecular phonon, the Hubbard repulsion prevails and the system is an insulator with a small Mott gap of $approx$ 0.2 eV.