It's been far too many years since I messed with controllers, etc, but hopefully someone else may come along that can help.
If you only have one controller connected to your PC it should be okay but if you have more than one... i.e pedals, etc, I think it depends on which one you connected first. I believe you can go into controllers (joysticks, etc) and alter their position via 'properties', but as I say, it's been many years since I messed with such stuff.
Failing that perhaps you could google it.