A mature wireless sensor network automation tool requires the implementation of different protocols for different topology and application scenarios to optimise the overall system performance. Focusing on the transport layer energy-aware routing function for the Tyndall Heterogeneous Automated Wireless Sensor (THAWS), embedding a reactive routing protocol, an energy-efficient proactive heuristic protocol and a distributed geographical routing mechanism on the Tyndall 10 and 25 mm nodes is proposed. Those protocols manage small, medium and large sensor applications adaptively, while the end users of the THAWS tool are transparent from protocol selection.