Here we examine the microscopic details of convective assembly, a process in which thin colloidal crystals are deposited on a substrate from suspensions of nearly monodisperse spheres. Previously, such crystals have been shown to exhibit a strong tendency toward the face-centered cubic structure, which is difficult to explain on thermodynamic grounds. Using real-time microscopic visualization, electron microscopy, and scanning confocal microscopy, we obtain clues about the crystallization mechanism. Our results indicate that the regions at which a growing crystal transitions from n to n + 1 layers can play an important and previously unrecognized role in the crystallization. For thin crystals, we show both from experiment and through simple modeling that these transition regions can generate specific crystal structures. In thicker crystals, the crystallization is more complicated, but the transition regions must still be considered before a complete understanding of convective assembly can be obtained.