The transport and structural phase dynamics exhibited by multilayer assemblies comprised of cyclic and linear alkanes are analyzed with reflection absorption infrared (RAIR) and temperature-programmed desorption spectroscopies. Infrared spectroscopy reveals that methyl group substitutions have a significant effect on the nature of the mode softening seen in the C-H stretching region for surface-bound cyclohexanes. The magnitude of the red-shifts seen increases with the degree of methyl substitution. The energetics of the surface binding do not correlate in a simple way with the magnitude of red-shifts seen in the RAIR spectra, however. We find instead that the strengths of the surface interactions are more directly correlated with both the size and shape of the molecule (with the latter presumably reflecting its ability to form a densely packed structure). We also find that the diffusion of molecules in a mixed hydrocarbon multilayer assembly is weakly activated, with substantial interlayer mixing being seen at temperatures significantly below the threshold for the desorption of the multilayer. The mixing, while driven by mass action, shows a pronounced bias for the surface binding of n-alkanes over cycloalkanes of similar molecular weight (e.g., n-octane is more strongly bound on Pt(lll) than is cis-l,3-dimethylcyclohexane). The data strongly suggest that attractive lateral interactions in the adsorbed layers lead to the biases seen in this surface-induced segregation. Thermal desorption spectra confirm this sensitivity and interestingly show multiple monolayer desorption features for cyclic alkane adsorbates when mixed in a monolayer assembly with an appropriate linear n-alkane. We suggest that the attractive lateral interactions in the monolayer lead to the formation of island domains and that the desorption kinetics appear to sensitively reflect this underlying rate/structure sensitivity.