Version 4 (newer) creates a "Virtual Xbox 360 Controller" and doesn't rely on DLL files inside game folders, making it better for modern games. Version 3 is often used for older titles.
Are you seeing a or is it just not recognized? I can provide more targeted steps. Xbox 360 Controller Emulator Toca Edit Xbox 360 Controller Emulator
Go to the [Controller #] tab, select settings, and assign your controller's buttons/axes to the virtual Xbox controller mapping. Version 4 (newer) creates a "Virtual Xbox 360