Superpotentials in ${cal N}=2$ supersymmetric classical mechanics are no more than the Hamilton characteristic function of the Hamilton-Jacobi theory for the associated purely bosonic dynamical system. Modulo a global sign, there are several superpotentials ruling Hamilton-Jacobi separable supersymmetric systems, with a number of degrees of freedom greater than one. Here, we explore how supersymmetry and separability are entangled in the quantum version of this kind of system. We also show that the planar anisotropic harmonic oscillator and the two-Newtonian centers of force problem admit two non-equivalent supersymmetric extensions with different ground states and Yukawa couplings.