First thing I would suggest is updating to a current version of cgminer. But if its working for you, then go ahead.
Secondly, you can use a -d argument to specify which gpu to use (I believe, dont use it myself). But default cgminer will use all devices it can find, this way can special -d 1 for example if you want to use gpu 1 instead of gpu 0.
Thirdly, you can set all of your gpu engine, fan, temp cut off, etc, just by using the arguments laid out on the cgminer page (whether it be command line, or conf file) located here
https://bitcointalk.org/index.php?topic=28402.0