Step 4: JoyToKey Basics
Make sure your controller is connected and open JoyToKey. The left hand side displays your configurations. You can multiple configurations to use for certain tasks (one for mouse movement, one for gaming, etc.). On the right hand side you'll see a long list that consists of "Button", "Keyboard", "Auto". This is where you define what the buttons (thumbsticks and directional pads count too) do. However, by default this list doesn't show every component of the Xbox 360 controller.
Click the tab on the very right labeled "Others". Here you can change the number of joysticks for this configuration. Adding more joysticks to configure allows the same customization of a separate configuration, but the you can only switch to different joystick configurations (Joystick 1, Joystick 2, etc.) temporarily (while a button is held down) where you can toggle between configurations (press once to switch, press again to switch back). To view the full range of buttons of the Xbox 360 controller click "Use Axes other than X and Y." and "Use POV switches".
Now, push the "Joysticks" tab to switch back to the list. You'll notice a lot more buttons are available for us to configure. Here's a rundown of what each button on the controller is listed as in the list.
Left Thumbstick Left = AxisX(<0)
Left Thumbstick Right = AxisX(>0)
Left Thumbstick Up = AxisY(<0)
Left Thumbstick Down = AxisY(>0)
Right Shoulder = Axis3(<0)
Left Shoulder = Axis3(>0)
Right Thumbstick Left = Axis4(<0)
Right Thumbstick Right = Axis4(>0)
Right Thumbstick Up = Axis5(<0)
Right Thumbstick Down = Axis5(>0)
Directional Pad Up = POV1:UP
Directional Pad Right = POV1:RIGHT
Directional Pad Down = POV1:DOWN
Directional Pad Left = POV1:LEFT
A = Button 1
B = Button 2
X = Button 3
Y = Button 4
Left Bumper = Button 5
Right Bumper = Button 6
Back = Button 7
Start = Button 8
Left Thumbstick = Button 9
Right Thumbstick = Button 10
(For clarification, the last two are achieved by pushing the left or right thumbstick in. They're called L3 and R3 on Playstation controllers, but I don't know if they have a name from Microsoft.)
There are plenty of other options, but what exactly they do I don't know. Using the guide above maps every button (except the Guide button) that I could find so I'm not worried.
The last step will give examples of configurations and provide the files that I use.