Well, I can't give you a definite answer, but here's what I'm doing:
In stock configuration, the green sensor goes before the cat, and the blue one after the cat. However, due to wiring lengths, apparently, the FS race header instructions tell you to reverse this when you install the sensors into the header.
Now the computer may only look at the difference between the two, or it may look at the green one as a reference, and the blue one for the "modified by the cat" value. I don't know. You might want to ask noresull in TEAM Tech.
I have a cheater harness on the way, and I plan on plugging it into the blue one, even though it's physically the first one down the pipe, just to be safe.