We present the results of extensive fully atomistic molecular dynamics (MD) simulations of tetracosane (C₂₄H₅₀) bilayer and trilayer systems adsorbed onto the basal plane of graphite. At low temperature, both layers of the bilayer exist in well-defined solid phases. With increasing temperature, the system exhibits separated smectic phases that eventually lead to melting. During this process, we observed a strong interlayer translational correlation and mobility between layers; however, the upper layer presents more intra- (chain) and intermolecular disorder because of a lack of confinement and a greater distance to the graphite substrate. Simulations of the perpendicular trilayer patch show that gauche defects provide the main mechanism for spreading of the bottom and outer perimeter of the patch in the solid, leading to the ultimate collapse of the patch with increasing temperature and formation of a flat (parallel) trilayer that melts at a higher temperature than the bilayer structure. The wide variety of structural order parameters, thermodynamic functions, and probability distributions we employed provide a clear picture of the roles of gauche defects, confinement, and interlayer correlation in the phases and phase transitions exhibited by these confined organic layers.