OK i found a work around of sorts but it definately not a very good solution as I have to create a .bat file for every Windows / Steam game I want to run.
In additional applications I add the batch file specific for that game and set it to start prior to the game starting..
EXAMPLE:
SoulcaliburVI.bat
start VirtualController.exe /load Custom.vcd /run /minimize
D:\Steam\steamapps\common\SoulcaliburVI\SoulcaliburVI\Binaries\Win64\SoulcaliburVI.exe
TIMEOUT 70
taskkill /IM VirtualController.exe /F
What this does is launch VirtualController.exe loading the dual xbox 360 controller profile I made, starts running, then minimizes it. Then next line tells it what to watch for. The timeout 70 gives the game 70 seconds to launch before taskkill starts watching to see if the program is still running or not. This is needed because some games take a while to start up. Without the timeout I kept running into the issue of the scirpt immediately killing VirtualController.exe because SoulcaliburVI.exe had not even started up yet, Then the last line kills VirtualController.exe when SoulcaliburVI.exe stops running using /f (force quit).
i am by no means a scripter and this is VERY sloppy, but it was the best solution I could cobble together until someone who knows what they are doing comes up with a better solution.
*EDIT* Oh I forgot to mention all the .bat files are residing in the same folder where VirtualController.exe is.