That means that I can't connect the GPIO port directly to the NyBoard because it is being used by the Hat. Serial communication is not a problem because I can get it over one of the USB ports. However... I need to figure out a way to get power to the PI from the main battery unit without using the GPIO pins.
Is there a way to do that without mounting an extra battery? Perhaps, is there a cable one could hook up to the NyBoard that has a USB connector on the other end?