Prior research has shown that spatial abilities are crucial for STEM achievement and attainment. The connection between the digital and physical worlds provided by embodied interaction has been shown to enhance performance and engagement in educational contexts. Spatial reasoning is a domain that lends itself naturally to embodied, physical interaction; however, there is little understanding of how embodied interaction could be incorporated into educational technology designed to train spatial reasoning skills. We propose several guidelines for gestural interaction design in spatial reasoning education games based on an empirical study with students at a local afterschool program using a custom-built computer game for training spatial skills. We present a series of gesture sets derived from an iterative design approach that are easy for children to acquire, show sufficient congruency to specific spatial operations, and enable robust recognition from the system. We also compared children's behaviors when playing the game with our gestural interface and a traditional mouse-based interface and found that children take more time but fewer steps to complete game levels when using gestures.