I have been seeing a lot of cornfusion on exhaust systems lately. Here is a little primer on what is out there and some of the terminology 
Stock Exhaust:
GT stock piping diameter is 2.388"
GS stock piping diameter is 2.129"
The ECU does not check, care about or look at the rear cat (the big round one under the center of the car) for anything.
GS Only:
The ECU only checks the front cats (the pair side by side up on the exhaust manifold, under the heat shield) and there are ways around that with little spacers.
GT Only:
The ECU only checks the front cats (one on the front exhaust manifold, the other on the rear exhaust manifold) and there are ways around that with little spacers.
Axle Back
Axle-back exhaust systems take advantage of the reasonably sized stock piping and non restrictive resonator after the catalytic converter. If you are on a budget, if you wont be going berserk with power mods, the axle back exhaust systems are for you.
They will go from just after the rear axle and back to the rear bumper:
Looks like this installed:
A Cat Back
A Cat Back exhaust will go from just after the catalytic converter back to the rear bumper.
Since there is no flange there you will have to cut the pipe and clamp the cat back exhaust on.
Here is a pic of the Magnaflow Cat Back clamped on:
The GT Magnaflow cat back piping is 2.5"
The GS Magnaflow cat back piping is 2.25"at the first bit before the resonator to slip over the stock piping and then to 2.5" for the majority of it.
Full Exhaust
A full exhaust would be something like the Injen that bolts on to the flange just ahead of the catalytic converter.
The Injen Full Exhaust which includes a metallic core high flow cat bolted on there:
Stock exhaust Manifolds and Y Pipe
The stock exhaust manifolds of the GT look like this. The pre-cats are welded into the stock manifold. Any headers will eliminate these pre-cats.
Front Pre-cat/Manifold:
Rear Pre-cat/Manifold
Stock Y-Pipe
When installing headers with O2 sensor spacers/anti-foulers, it does not matter what sensor goes in what hole. Whatever works best with the cable routing is the only concern. However it is very important that the spacers are installed under the 2nd O2 sensors, the ones with the black wire and the grey connector.
On cars with a more restrictive exhaust system you will need a spacer with a smaller hole in it. With a more open exhaust you will need a spacer with a bigger hole to get more fumes to the sensor. We sell spacers with smaller holes. It is easy to make the holes larger, very difficult to close them up if needed. If you install a spacer and get a SES warning light… FREAK THE EFF OUT AND RUN TO THE NEAREST MESSAGEBOARD AND TELL EVERYONE “OMG HtE hEX0RZ MY SES LIG4T IS ON!!!!” .-~*~-. Not really. It is totally annoying. Chill. Just check the code and if the code says the cat is below efficiency or has low voltage, open the hole a little.
On a GS the spacers go in the down pipe piece, not the headers.
Cat Funny Business:
The ECU does not check, care about or look at the rear cat (the big round one under the center of the car) for anything.
The ECU only checks the front cats (the pair side by side up on the exhaust manifold, under the heat shield) and there are ways around that with little spacers.
If the smog man knows that there is supposed to be a cat there and does not see one there, dude will not pass it visually (at least not with out visualizing an extra $100 bill or two).
If the front cats are in place and working then it _should_ pass a tail pipe test with out a main cat.
The SES light being off and no stored codes for emissions things is essential to passing a smog test and that requirement would be satisfied.
Mike W
Stock Exhaust:

GT stock piping diameter is 2.388"
GS stock piping diameter is 2.129"
The ECU does not check, care about or look at the rear cat (the big round one under the center of the car) for anything.
GS Only:
The ECU only checks the front cats (the pair side by side up on the exhaust manifold, under the heat shield) and there are ways around that with little spacers.
GT Only:
The ECU only checks the front cats (one on the front exhaust manifold, the other on the rear exhaust manifold) and there are ways around that with little spacers.
Axle Back
Axle-back exhaust systems take advantage of the reasonably sized stock piping and non restrictive resonator after the catalytic converter. If you are on a budget, if you wont be going berserk with power mods, the axle back exhaust systems are for you.
They will go from just after the rear axle and back to the rear bumper:

Looks like this installed:

A Cat Back
A Cat Back exhaust will go from just after the catalytic converter back to the rear bumper.

Since there is no flange there you will have to cut the pipe and clamp the cat back exhaust on.

Here is a pic of the Magnaflow Cat Back clamped on:

The GT Magnaflow cat back piping is 2.5"
The GS Magnaflow cat back piping is 2.25"at the first bit before the resonator to slip over the stock piping and then to 2.5" for the majority of it.
Full Exhaust
A full exhaust would be something like the Injen that bolts on to the flange just ahead of the catalytic converter.

The Injen Full Exhaust which includes a metallic core high flow cat bolted on there:

Stock exhaust Manifolds and Y Pipe
The stock exhaust manifolds of the GT look like this. The pre-cats are welded into the stock manifold. Any headers will eliminate these pre-cats.

Front Pre-cat/Manifold:

Rear Pre-cat/Manifold

Stock Y-Pipe

When installing headers with O2 sensor spacers/anti-foulers, it does not matter what sensor goes in what hole. Whatever works best with the cable routing is the only concern. However it is very important that the spacers are installed under the 2nd O2 sensors, the ones with the black wire and the grey connector.
On cars with a more restrictive exhaust system you will need a spacer with a smaller hole in it. With a more open exhaust you will need a spacer with a bigger hole to get more fumes to the sensor. We sell spacers with smaller holes. It is easy to make the holes larger, very difficult to close them up if needed. If you install a spacer and get a SES warning light… FREAK THE EFF OUT AND RUN TO THE NEAREST MESSAGEBOARD AND TELL EVERYONE “OMG HtE hEX0RZ MY SES LIG4T IS ON!!!!” .-~*~-. Not really. It is totally annoying. Chill. Just check the code and if the code says the cat is below efficiency or has low voltage, open the hole a little.
On a GS the spacers go in the down pipe piece, not the headers.

Cat Funny Business:
The ECU does not check, care about or look at the rear cat (the big round one under the center of the car) for anything.
The ECU only checks the front cats (the pair side by side up on the exhaust manifold, under the heat shield) and there are ways around that with little spacers.
If the smog man knows that there is supposed to be a cat there and does not see one there, dude will not pass it visually (at least not with out visualizing an extra $100 bill or two).
If the front cats are in place and working then it _should_ pass a tail pipe test with out a main cat.
The SES light being off and no stored codes for emissions things is essential to passing a smog test and that requirement would be satisfied.
Mike W