I don't know what kind of IT they did back in the days when there was only one thread running.
I would imagine that there is a lot of actual debugging of the circuits, though. http://www.history.navy.mil/photos/images/h96000/h96566k.jpg
EDIT Oops Multi-threaded computers were around in the 50s: http://people.cs.clemson.edu/~mark/multithreading.html
Duplicating damaged punch cards