You have the option to feed power through a micro-USB as you normally would to the RaspberryPi, or through a standard spaced header.
The top header has connections for the power button and an LED that will be ON while power is ON, and will fade in and out while shutdown is in progress. The output header has INPUT and OUTPUT signals that connect with the Pi’s GPIO, and of course the power OUTPUT to the Pi. There 2x 5V and 3xGND outputs, and four standard mounting holes.
When the button is pressed the first time the LED turns ON and power will flow from INPUT to OUTPUT and turn the RaspberryPi ON. The BOOTOK signal is turned HIGH by RaspberryPi via the shutdowncheck.sh script which you need to install. This is how ATXRaspi knows that the Pi has successfully booted. The SHUTDOWN signal is turned HIGH when ATXRaspi is asking RaspberryPi to shutdown or reboot. The same script will listen to this signal and issue either a shutdown or reboot depending on how long this signal is kept HIGH.