In the past I have had to prepare the 4136 outside Proseries, then enter the amount of the credit on the 990-T, (when I did it a few years ago) I had to prepare a -T just to record the credit and get the refund. I think at that time we were mailing in the return. Not sure if you can attach a pdf to a 990-T or not.

There was no place on the 990 to enter credits. I haven't looked in the last couple of years to see if it is still the same, as I don't have that situation any more.