After browsing several forums, including the steam discussion threads, I noticed that a lot of players were finding difficulty in setting up their X360ce settings for controller support. After several hours of faffing around on the steam discussion board, and browsing several of the topics already posted here, I realised the Issue.

The Witcher 3 comes complete with controller support as standard, but when you run X360ce, usually it creates it's own "Xinput1_3.dll" file into the bin folder, which normally overwrites the standard one. Every time I ran X360ce, I assumed that the file was being created by the application. Turns out, this isn't the case.

If you're having difficulty getting your controller to be recorgnised, every time you run X360ce or your controller isn't responding after having run the application; follow these steps.

1. Back up the "Xinput1_3.dll" file in your bin folder.(this is just incase things go wrong and you want to start again)
2. Delete "Xinput1_3.dll" file.
3 Run X360ce from your bin file.
4. X360ce will ask if you want to create a "Xinput1_3.dll" file, select "create".
5. Scan for settings.

Your controller should now be recognised. If you're running a 64bit version, and the controller still does not respond, go to game settings>my game settings and check the box on the Xinput settings on the right, that it's on v9.1 (when first running X360ce it listed as 32-bit)

Before running your game however, check the button mapping for your controller. When I checked it, I realised I had to change the button layout, as the configuration found for me was incorrect and had mixed up the A, B and X buttons with one another.

I hope this helps anyone having trouble with setting up their controller :)