If your hardware has a preset configuration in X-Plane, the joystick settings screen will show an image of the device and have many of the axes and buttons already configured. If X-Plane does not present an image of your device, you will need to set all axes and buttons manually. See the section “Configuring Flight Controls” in the manual for step by step instructions.
If buttons appear to be missing from the list in the joystick settings screen, check for another option under the “View” drop down box. Additional buttons may be shown on an image of the device at a different angle.
If you have more than one piece of USB hardware plugged in, use the “Device” drop down menu to switch between them to set up all buttons and axes. Make sure each type of axis (pitch, roll, etc) is only assigned once among all the devices.