I assume you're talking about the Pololu 1201
http://www.pololu.com/catalog/product/1201 modules? Many people use those with MakerBots as they are much quieter and run cooler than the stock (Gen 3) hardware.
In my experience running them on a MakerBot and a Mendel with NEMA 17 motors, they run cooler than stock but still too hot for my taste with the tiny included heatsink. I imagine a small 12 or 24V fan would keep things cool enough for use, though another big factor is tuning the drivers. The potentiometers are convenient to use, but never as precise as popping in a fixed value resistor would be. I doubt they have some of the same hardware protection as the more expensive guys (Keling, Gecko) but for $12.95, how can you complain?
For reference, this is the guy I'm using on my Makerbot:
http://www.thingiverse.com/thing:4861