Atomic spins are natural carriers of quantum information given their long coherence times and the our ability to control them with applied coherent electromagnetic fields. In this talk I will review our recent progress in the design of quantum control protocols and their implementation in the laboratory including: preparation of arbitrary spin states in a larger dimensional hyperfine manifold, quantum state reconstruction via continuous polarization measurement, design of pulse sequences to implement qudit unitary maps, and controlled quantum transport in optical lattices.