There is an increasing demand in designing heterogeneous networks, where various low-power wireless radios such as ZigBee and Bluetooth devices coexist, while sensing devices may generate traffic with different intervals. In this work, we devise an architecture of a cross layer controller, encompassing a software defined radio at the data plane to manage radio access, and a software defined networking at the control plane to manage data flow, while considering the application requirements. The overall architecture aims at simplifying system management and network re-configuration, while providing better network performance.