A Joystick (or your RC transmitter connected as a joystick) can be used to control your aircraft in the simulator or via the modem in real flight using Input2Ivy.
You should always calibrate your joystick, so that you have zero input when the sticks are centered, etc...
Install the joystick and optionally the jstest-gtk packages:
sudo apt-get install joystick jstest-gtk
Use the graphical jstest-gtk tool (or the commandline jstest) to view/edit your joystick calibration and axis/button mappings.
Your calibration and mapping will only be lost once you unplug the joystick, so store your configuration:
sudo jscal-store /dev/input/js0
If you replug your joystick the next time, udev should take care of automatically loading the appropriate configuration.