Ultracold neutral atoms confined in optical dipole traps have important applications in quantum computation and information processing, quantum simulators of interacting-many-body systems and atomic frequency metrology. While optical dipole traps are powerful tools for cold atom experiments, the energy level structures of the trapped atoms are shifted by the trapping field, and it is important to characterize these shifts in order to accurately manipulate and control the quantum state of the system. In order to measure the light shifts, we have designed a system that allows us to reliably trap individual 87Rb atoms. A non-destructive detection technique is employed so that the trapped atoms can be continuously observed for over 100 seconds. Single atom spectroscopy, trap frequency measurements, and temperature measurements are performed on single atoms in a single focus trap and small number of atoms in a 1D optical lattice in order to characterize the trapping environment, the perturbed energy level structures, and the probe-induced heating. In the second part of the thesis, we demonstrate deterministic delivery of an array of individual atoms to an optical cavity and selective addressability of individual atoms in a 1D optical conveyor, which serves as a potential candidate for scalable quantum information processing. The experiment is extended to a dual lattice system coupled to a single cavity with the capability of independent lattice control and addressability. The mutual interactions of atoms in different lattices mediated by a common cavity field are demonstrated. A semi-classical model in the many-atom regime based on the Jaynes-Cummings model is developed to describe the system that is in good qualitative agreement with the data. This work provides a foundation for developing multi-qubit quantum information experiments with a dual lattice cavity system.