it depends on the game. If memory serves me right, if the game uses DirectInput, the game will poll for changes using a virtual device. As long as your device can output a similar virtual device code, the game wont know the difference.

For example, I play TF2 often. TF2 and all source engine games use bindings to bind the actions to virtual keys. The virtual key code is DirectInput and win32 keycodes. I bind the same actions on my keyboard to my MOUSE3 and MOUSE4 buttons. So in a way, i am using 2 input devices for the same action. How this is possible is because the developers don't poll the device directly, rather they use virtual key codes.

You will need to check how to remap the inputs for each device depending on the device. I don't think there is a general solution which works for all devices.

GlovePIE is a Windows program that allows writing scripts to map inputs to other inputs.

For example, if you have two joysticks with two buttons each, then you can use something like this:

Joystick1.Button3 = Joystick2.Button1
Joystick1.Button4 = Joystick2.Button2

to consolidate the two.

Obviously, your script's gonna need a lot of tweaking, and this is mainly for programmer types who can be bothered to understand stuff like this.

GlovePIE is pretty powerful once you know how to work it, however.