Tin phthalocyanine (SnPc) has been studied on superconducting Pb(100) using scanning tunneling microscopy and spectroscopy. Isolated molecules adsorb with their Sn ion below (SnPc↓) or above (SnPc↑) the molecular plane. These geometries lead to different adsorption sites, molecular orientations, and energies of the frontier orbitals. A transition from SnPc↑ to SnPc↓ can be induced by extracting electrons from a single molecule. Density functional theory (DFT) calculations reproduce the observed geometries and indicate that a positive charge of the molecules facilitates the ↑-↓ transition. The molecular orientations are essentially determined by the σ-orbitals on the peripheral N atoms and exhibit minimum distances of their lone pairs from the nearest Pb substrate atoms. This binding scheme, which implies a direct relationship between the adsorption site and the molecular orientation, is consistent with many previous observations on other substrates. In molecular islands, single molecules can be forced onto less favorable adsorption sites. This leads to a strong Yu-Shiba-Rusinov state of SnPc↓ at top sites revealing an induced molecular spin. Similarly, the spin observed from SnPc↑ on hollow sites is quenched by their conversion to SnPc↓. The calculated lowest unoccupied molecular orbital energies are consistent with these spin-state transitions.