Thermoelectric coolers (TECs) are horrendously inefficient (slightly better now than a decade ago, but not really by that much). Cooling a hunk of inert material is the easiest. Cooling and controlling the temperature of an active, power dissipating device is harder. Much harder.
Example: back in the optical telecom boom days, I was working on the packaging for an optical switching device. The main designers were all excited because they had worked a design that integrated the active optical material and the rf drive circuits onto a little substrate perhaps a square centimeter or so. I asked for the specs on how cold, and how much power the circuits would need, and they said is was only 10W, and it didn't need to be that cold, just controlled.
Well, commercially available TECs were roughly 10% efficient at that time. So, to pump 10W off the substrate required 100W of power to the TEC. This in turn meant that 110W was dumped to the heatsink at room temperature. That meant a roughly 4"x4" TEC, and a huge honking 6"x6" heatsink with giant fan. So, that beautiful tightly integrated device meant a giant package.
What does this mean for you? Well, you stack TECs in order to make your cold object colder. But it comes at a big penalty in how much power your "cold" object is allowed to expend. That first stage is only 10% efficient. The second stage has to be sized so that all the power of the device AND the first TEC can be pumped through it, and at only 10% efficiency again. Ouch. In the case above, a second stage would have been pumping 110W, so it would have needed about 1100W to pump that, meaning 1210W overall. Your efficiency goes to hell with stacked TECs - each additional stage has to inefficiently pump the inefficiencies of all the previous stages.
If you want to be as efficient as possible, use a single stage. That will limit your ultimate temperature, but will pull the most power off the cooled device. If you want the lowest temperature possible, stack your TECs, but understand that the maximum power your can dissipate will drop like a stone.