Not sure. When I had to do it was for a private school that filed a normal 990, but had to file the 990-T to get the fuel tax credit on form 4136. All that was on the 990-T (As I Recall) was the credit amount and the 4136 attached.

You will probably need to look around on the 990-T and see if you can find a place for the withholding. That's as close as I can get you.