I'm afraid I can't help specifically with the X45, but I've just finished setting up my own joystick, so here's the controls I'm hoping are useful :):
Fire (guns, bombs)
Gunsight range (up, down)
Trim (ailerons, elevator, rudder, reset)
Wheel brakes (left, right, both)
WEP
NVG
Radio PTT
Eject
Kneeboard (on/off, next, prev, mark point)
Labels on/off
View (zoom, look around)
There's some stuff people seem be putting on their joysticks that you can also just click on in the cockpit, up to you if you want to include them:
Gear
Flaps
Propeller RPM
Radiator
Mixture
Supercharger
Gunsight mode
Landing lights
Parking brakes
Canopy
Other people's setups:
http://forums.eagle.ru/showthread.php?t=103190&highlight=setup
http://forums.eagle.ru/showthread.php?t=87578&highlight=setup
http://forums.eagle.ru/showpost.php?p=1468387&postcount=6
http://forums.eagle.ru/showpost.php?p=1455218&postcount=10
http://www.digitalcombatsimulator.com/upload/iblock/58f/Description.jpg