A mixture of large and small Lennard-Jones particles is studied; in the study we focus on the relations among temperature, packing, structure, and transport in the supercooled state. As the temperature decreases, one sees increasing component separation, and local ordering. Clusters consisting of only small particles grow in size with time and cooling; the dominant local structure in those clusters is hexagonal. The rest of the system, including almost all large and some small particles, remains amorphous, with local order dictated by the geometry of dense packing of mixed large and small particles. To study these effects independently, we modified the conventional model by managing the relaxation of large particles. At low temperatures, the diffusion of small particles dramatically decreases when the large particles are frozen. An interpretation of these findings based on the local rearrangement kinetics is proposed.