Furthermore, the LED when the jumper is out should be the following....

RED LED - Gyro Off (Transmitter ATV should be at 0)
AMBER LED - Gyro ON in RATE Mode (ATV is your gain setting - ie: -20 = 20% gain in Rate mode)
GREEN LED - Gyro ON in HEADING HOLD Mode (ATV of +20 = 20% gain in Heading Hold mode)

You can adjust each axis individually with the use of a PC. For example, if you wanted more gain on the ailerons, but wanted to leave the rudder and elevator at a lower setting.