Hey SF,
To control a TECs wattage you just have to adjust the applied voltage - the amps will follow voltage (as voltage increases, so will the current draw). Now doing so with a 3-way switch might not be so easy. You would have to have two power (voltage) sources one high, one low and switch between them.
Another method you can use if you are building a water-chiller with multiple TECs is to switch on 1, 2 or 3 TECs for low, medium and high cooling. I tried this with my two TEC chiller once. One TEC is powered on all the time - basic cooling. I used a temp probe from a DigiDoc5 to monitor CPU waterblock temps and when they exceeded the programmed trip point on that channel of the DigiDoc, the fan output associated with that temp probe turned on. Instead of turning on a fan, the DigiDoc triggered a high current solid state relay which turned on the second TEC power supply - high cooling. You could expand the theme to three TECs or more depending on your goals and budget...
Of course you don't have to use an automated controller (DigiDoc - now that's a strectch) you could just use toggle switches.
Good luck,