By providing interactive broadband services to geographical areas underserved by terrestrial infrastructure, multi-beam satellite systems play a central role in future wireless communications. Targeting the terabit throughput requirements in satellite communications, we introduce a cognitive radio-based high-throughput satellite (HTS) system architecture where full frequency reuse is employed among beams. Moreover, by analyzing the characteristics of the considered architecture, we discuss the design challenges of radio resource management in cognitive HTS systems exposed to both intra-system and inter-system co-channel interference. Furthermore, to combat interference with low overhead, we propose a generic interference-aware resource management framework based on joint spatial division and multiplexing (JSDM). Under this framework, user grouping along with two-stage precoding is studied to achieve substantial improvement in the overall system throughput. Finally, some future research directions and challenges are also given.