Since Arduino Mega ADK is using the same ATmega2560 as on Arduino Mega, there's no USB module built-in the MCU itself. So you cannot communicate directly with the chip via USB, which I think is what you want to achieve. It uses other chips to establish the USB connection.
Arduino Mega ADK offers two ways to communicate via USB. One is through the ATmega8U2 and appears as virtual com port in computer. This is the same as using Arduino Mega's USB port to communicate with USB host (computer). Another way is through MAX3421E and appears as USB host. It allows communication with other USB devices.
Please refer to
"Communication" in Arduino Mega ADK's official page.