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I personally never use the stock cooler. I once built someone a budget system and used a stock cooler and you know what happened? Didnt cool down the cpu enough and it ended up frying the board.
As for fans. I never use stock case fans. I go to sites and purchase the size fan i need with the best CFM (how much air can be pushed in a cubic foot per min) rating i can find. The fans may be a little on the noisy side but id rather have cooling then silence and high temps.
Good termal compound will drop your temps down, along with the type of core being used in your cpu and the amount of nanometers on the circuity.
I always keep my tower on the desk it does help the airflow especially if you have side vents. If you dont have side vents and just have the front intakes and hte back outakes then the encapsulation will not really matter. But like i said if you have side vents your gonna want to put it in a clear spot and keep the room cool. Not freezing just comfortable.
Dont use it on the floor if you have a carpet, carpets collect dust and all kinds of nasty stuff. Which your front intake fans will just suck up.
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