SNUGLITE-III, consisting of two 3U CubeSats, is designed to perform scientific missions which involve analyzing the Earth's atmosphere using GPS Radio Occultation (RO) data collected through autonomous formation flying. Both satellites are initially jointed and ejected together from a 6U P-POD (Picosatellite Orbital Deployer). Subsequently, after completing initial operations, they undergo inter-satellite separation and initiate a formation flying operation. In the SNUGLITE-III mission, relative motion of the two satellites are controlled without any propulsion system, utilizing aerodynamic forces. Therefore, a detailed analysis of the relative motion occurring after separation is crucial. This paper investigates the relative motion of two satellites based on the direction of inter-satellite separation. The analysis integrates both Hill-Clohessy-Wiltshire (HCW) equations and the orbital element changes due to the separation and J2 perturbation. Characteristics of the relative motion based on the separation direction are summarized, and orbit propagation simulations are conducted to validate the analytical findings. Based on these results, an appropriate separation direction for the SNUGLITE-III mission is selected, satisfying the requirements for its autonomous formation flying mission.