We analyze theoretically the dynamics of an atomic double-well system with a single ion trapped in its center. We find that the atomic tunneling rate between the wells depends both on the spin of the ion via the short-range spin-dependent atom-ion scattering length and on its motional state with tunneling rates reaching hundreds of hertz. A protocol is presented that could transport an atom from one well to the other, depending on the motional (Fock) state of the ion within a few milliseconds. This phonon-atom coupling is of interest for creating atom-ion entangled states and may form a building block in constructing a hybrid atom-ion quantum simulator. We also analyze the effect of imperfect ground-state cooling of the ion and the role of micromotion when the ion is trapped in a Paul trap. Due to the strong nonlinearities in the atom-ion interaction, the micromotion can cause couplings to high-energy atom-ion scattering states, preventing accurate state preparation and complicating the double-well dynamics. We conclude that the effects of micromotion can be reduced by choosing ion-atom combinations with a large mass ratio and by choosing large interwell distances. The proposed double-well system may be realized in an experiment by combining either optical traps or magnetic microtraps for atoms with ion trapping technology.