Usually, carpal tunnel and A/L/S appear different on an EMG and NCS (they typically do both tests). Carpal tunnel (CTS) will often show slow nerve transmission on an NCS in both motor and sensory nerves; since A/L/S doesn't affect sensory nerves or (at least in the early stages) slow nerve transmission speed, this can be used for a differential. In addition, A/L/S will typically have signs of denervation (positive sharp waves and fibrillations), while CTS doesn't unless it's really bad.
Typically, the only time CTS and A/L/S are confused is during the neuro exam, when weakness in the muscles of the hand is noted. If there's no weakness, there's no A/L/S. If there is weakness, it's still far more likely to be CTS, which is present in (by some estimates) 2–3% of the population. That's a lot more people than have A/L/S.
BTW, CTS was on Jeopardy last night. They showed someone using a segmented keyboard (appears to be the one I have in my office) and asked about the syndrome that causes pain in the wrist. If you've got pain, it makes it even less likely you have A/L/S.