An important feature of the deposition process in the systems considered here was polymorphism. Extensive sampling of the configurational space led to multiple configurations with similar energies for both the helicene enantiomers and for coronene. The highly dynamic behaviour of the molecular backbones and of the adatom patterns at non-zero temperatures further expands this configurational complexity. These findings improve our understanding of the impact surface irregularities have on the adsorption of PAHs on metal substrates, and thus provide an important complement to experimental results in these systems.