Nothing at all to be confused about. The IAT sensor needs to go between the blower and the engine, but after the intercooler/aftercooler. Simple as that, I dont care what some shops directions say, thats how it is supposed to go.
Why can I say this? Because I tuned my old turbo 04 GT myself, and I know the importance and role the IAT sensor plays in things. It NEEDS to know the intake inlet temps just before it goes into the engine so it knows when and how much to start pulling timing if the charge is too hot.
Now if these were a factory supercharged setup (L or cobra) and you were converting to a centri...then the IAT 1 should go before the blower (or just off somehwere so it knows true outside air temps) and the IAT 2 should go in the charge pipe or just stay in the intake manifold like it is from teh factory. IAT 1s in their case does nothing with the timing....just is used for refrence so it knows what the pre blower temps are, that way it expects IAT 2s to be a little higher if its hot outside. If its sensing 12* air IAT 1 and your IAT 2s are 200*s, then it should throw a code because it knows somthing is wrong. IAT 2 is what is actually used by the EEC to determine when to pull timing in the case of the cobra and Lightning.
yea more information than you needed, but you get the point