This sounds logical, why not allow users to simply add executables themselves and link appropriate settings to them ?
The only difficulty i can see is being able to bind them in the game.
How about a small window that pops up the first time you launch a new title (or via a button in Infinite Screen) which allows controlling the vJoy device manually.
Some options to pause the data from EyeX to the vJoy device, and 4 buttons to force full vJoy deflection up/down left/right.
Create the window with the always on top attribute and it should stay on top nicely.