We study the lateral and transverse diffusion of amphiphiles in two-component bilayer membranes, using a coarse-grained model for amphiphilic molecules and combined Monte Carlo-Molecular Dynamics simulations. Membrane structural properties, such as the mean thickness, are also measured. The dependence of such properties on membrane composition, inter-molecular interactions, and amphiphile stiffness is determined. In particular, we show that addition of shorter amphiphiles drives the model membrane towards a more fluid state, with increased amphiphile lateral diffusion rates. These results can be understood in the framework of a simple free-volume model. Furthermore, we observe an increase in the trans-membrane diffusion when the interaction energy of amphiphiles with their neighboring molecules is decreased.