User-centric joint transmission coordinated multipoint (JT-CoMP) has been shown to enhance the capacity of terrestrial cellular systems, by overcoming cell-edge interference. This paper investigates how JT-CoMP can be extended to a new high altitude platform (HAP) system architecture by exploiting a phased array antenna, which generates multiple beams that form cells, each of which can map on to pooled virtual base-station equipment, thereby replacing multiple terrestrial cell sites. The strategy to implement CoMP is designed to best enhance the user experience at the edge of the HAP cells, including the overall performance of the system. Methods to overcome the known tradeoff for JT-CoMP between carrier-to-interference plus noise ratio (CINR) gain and loss of capacity accessible to the users are considered. Two different methods of identifying non-CoMP and CoMP users are introduced based upon the centralized CINR threshold and flexible CINR threshold approaches. For the bandwidth allocation technique, two approaches are used: full bandwidth (FBW) and half bandwidth (HBW). These four approaches are combined, delivering the FBW, HBW, Flex FBW, and Flex HBW schemes that are used to control the JT-CoMP. It is shown that 57% and 45% of users gain benefit from the use of HBW and FBW, respectively. Overall, the schemes based on the flexible CINR threshold approach provide the best balance between loss and gain of the user capacity, while the centralized CINR threshold-based schemes performed well, beneficiary up to 57% of the users, but with the drawbacks of a higher percentage of losing users.