Joysticker Pro utilizes a map file that converts any joystick you may have to a standard gamepad configuration. Basically it ends up looking like an XBOX360 controller, and this makes the button remap scripts you write portable across any joystick.
While Joysticker Pro already has many of the more common joysticks configured, it is possible yours might not be in the built-in database. You may need to create one of these mapping files which is just a way to tell Joysticker Pro which hardware buttons you want to map to a given gamepad button name. The easiest way to generate a new mapping is to start Steam in Big Picture mode, configure your joystick and then look in config/config.vdf in your Steam installation directory for the "SDL_GamepadBind" entry. Copy it without the quotes and put it in the userControllerDb.txt file located in the Joysticker Pro directory. The mapping format is human-readable and you could also do it by hand if you don't have Steam. I'll try to get a video up on how to do this within the next couple of days.