[RyanW]

Yes, the joystick is powered. The OI is plugged into the competition interface thing the whole time. However, at the beginning of the autonomous code, all of the OI are set to neutral (you can't change that part), and so are of no use to you. You can, however, receive input from whatever you have on your robot, including onboard digital I/O switches if you want to switch between autonomous modes beforehand. You can also get sensor input and send output to motors as normal.