I use ATI Catalyst Control Center, it's under OverDrive tab. If you haven't overclocked and have good air flow in your case, then you should be fine in Auto, unless the room temp is high. If it is running too hot, you can try underclocking it, but that will sacrifice some of the performance.
Be warned, however, that setting your fan at high speeds constantly will decrease the life of the fan. Hopefully you will upgrade your GPU long before your fan fails. It may also be possible to get improved fans and heatsinks for your graphics card if you are really serious about it. In general you shouldn't worry too much since these cards are usually rated to run at very high temps.
Also, your computer should automatically stop if temperatures get excessively high.