Avoiding overheat XFX 6970 Crossfire
So, I've been running into problems with my new computer and it's crossfire XFX 6970's. The cards tend to run hot, at times too hot such as playing BC2 and I wasn't able to see the temperature's after 45 min of gameplay when my PC froze from I'm assuming the graphics cards overheating, sometimes they peak out at around 102c. So, looking online I decided to manually set my GPU fans with the ATI Overdrive but, I got a little worried using them. I have the fans set to 65% and my cards are idling much cooler but the problem now is my cards are much louder which I am worrying that could cause harm to them. I tried setting the fan speed to 100% but it was so loud I was afraid of something breaking. Is this normal when turning on fans manually.
Increasing the fan speed will make the card run a lot louder. The fans might not last as long if you have them running at high speed, but cranking them up will not damage the card. It sounds like you really need the fans cranked up anyway, 102 degrees is not an acceptable load temperature for any GPU. The fact that you have to crank up the fans to prevent that seems to indicate that the cooler probably isn't seated properly, or had the thermal compound improperly applied. Either that, or you have very poor airflow inside your case.
How many case fans do you have? How many are pulling air in, and how many are pushing air out? Are there any cables or other expansion cards blocking your video card's airflow? If airflow is adequate, your options are to either try to reseat the cooler and reapply the thermal compound yourself, or RMA the card. Given the fact the card probably still is under warranty, I'd get it replaced. The stock fan speeds should be able to cool the GPU enough that it won't hit critical temperatures like your card is.
As supernova1138 metioned, first, might be a good idea to change the thermal paste.
Assuming that the cards are the XXX edition (where the hot air is pushed out of the case) id suggest making a canal of cold air for the cards air-intake.
Apart making some work around your case, those are your 2 only viable options (or getting an aftermarket cooler for them assuming they are compatible with the PCB design).