Try this fix for USB headset sound in Prepar3D, at least in Windows7. See the attached upload.
In "Control Panel", go to "Hardware and Sound", then "Sound". In the popup window I selected my USB headset as "Default Communications Device" and applied those settings. Upon opening P3D, I had ATC sound in my headset, and all other sounds through my 5.1 surround speakers. I don't have a 3rd-party ATC program, so I don't know if the USB microphone works.
Rob