It's only in MDT Workbench you can sort drivers how you want them to. In the actual file folder structure in Windows, everything gets lumped togtether under the Out-of-Box Drivers folder. If you start change how MDT Workbench put in in the actual file folder, you will mess things up. Don't do that.
I use Johan Arwidmark's Total Control when it comes to driver management in MDT. See --> http://deploymentresearch.com/Research/Post/325/MDT-2013-Lite-Touch-Driver-Management