Magnetic molecules adsorbed on a superconductor give rise to a local competition of Cooper pair and Kondo singlet formation inducing subgap bound states. For Manganese-phthalocyanine molecules on a Pb(111) substrate, scanning tunneling spectroscopy resolves pairs of subgap bound states and two Kondo screening channels. We show in a combined approach of scaling and numerical renormalization group calculations that the intriguing relation between Kondo screening and superconducting pairing is solely determined by the hybridization strength with the substrate. We demonstrate that an effective one-channel Anderson impurity model with a sizable particle-hole asymmetry captures universal and non-universal observations in the system quantitatively. The model parameters and disentanglement of the two screening channels are elucidated by scaling arguments.