I found this neat little trick from a comment made on DemonX's Youtube video tutorial regarding how to get RemoteJoy working:
Now assuming you've got the two plugins enabled and the USB Host files installed then do the following:
1: Run the game you want to play.
2: Load the savefile or start the new game.
3: When your in gameplay mode then load up Start-USBHostFS_PC.bat
4: Then open whichever screen mode you want. (I prefer Start-RemoteJoy-FS.bat)
5: Finally just hit F5 with the remotejoy window open and you can play away!
This application is great!:Punk: