UART and USB UART are same things fro Linux, so you just need to change the /dev/ttyXXX name when launching ArduPilot with the name that will be given to the adapter port.
sudo ArduCopter-quad -C /dev/ttyAMA0UART and USB UART are same things fro Linux, so you just need to change the /dev/ttyXXX name when launching ArduPilot with the name that will be given to the adapter port.
sudo ArduCopter-quad -C /dev/ttyAMA0