Methods, devices, and systems for commissioning and programming a network of wireless devices are disclosed herein. These can include utilizing a commissioning tool having a directional radio frequency antenna, a microprocessor, and memory. The commissioning tool can function with a Smartphone, or be a stand-alone device. The commissioning tool can program wireless devices without direct physical access or direct line-of-sight from the commissioning tool to the device. The commissioning tool can establish network connections with a “query,” “wink,” “ping” protocol, connecting devices that control HVAC, water heating, and lighting systems wirelessly with a border router that can be for upload data collected by devices to the Internet. The method can also include collection, analysis, and illustrations of building system performance data on web-based software.