A neutral atom interacting with a single mode of a high finesse cavity provides an opportunity to study uncharted quantum mechanical systems and to explore the field of quantum computing and networking. Ranging from being a deterministic single photon source to a coherent storage unit for quantum information, a strong coupling cavity QED system has proven to be a powerful tool. In this thesis, single atoms are deterministically delivered over long distances and probed in an optical cavity. Once in the cavity, a single atom is stored and continuously observed for over 15 seconds. Progress towards using atoms in the cavity to produce entangled photon pairs is presented. Dual 1D optical lattices are implemented to create a foundation for advancements in two qubit quantum operations and entanglements.