Once you have a bootable DOS disk, you need to put the DOS Thrustmaster files on it. Ideally, these files should all go in a \TM directory off of the root. For example, if your thumbdrive is E:, then you should put the Thrustmaster files into E:\TM. If you unzip the files directly onto your drive with WinZip (or similar), you'll find that they expand into the correct folders automatically.
Thrustmaster released several versions of their software. I myself have the F-16 FLCS software all zipped up and downloadable for you here at the bottom of this page. It will work with the FLCS by itself, and when hooked up to a WCS Mk II or a TQS throttle. I think it will also work the the F22-Pro, but I need to do more research.
To start the software, just change
directories into the TM folder (that is, type "CD \TM" without the
quotes) and then type "tm" (also without the quotes) to run the main
Thrustmaster DOS front end.