You knew enough that your car had a check engine light and went out and got a scanner. Great! I would at least figure that even a novice (such as myself) would read the directions that came with the scanner or knew that the scanner must provide you with some sort of information that could be passed on to others for help.
Read the directions on the scanner, plug it into the car and pull the codes. Post back here with the results and we can/may help you out. But your first post was like, "Well, I bought a new car and it came with these keys? Anyone know how they work?" Like I said, it's like putting the cart before the horse. Give us something to work with other than your symptoms to help narrow down the problem with your LS.
If you are wondering, the OBDII port (which the scanner plugs into) is just below the kick panel, below the steering column. You have to get down in there to see it, but it's there.