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Fan setup question.

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This case won't be exactly like yours but the principle is the same: The fans should be oriented to move the air in one direction from front down low to back and top up high. Excellent choice for a case, by the way.
 

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This case won't be exactly like yours but the principle is the same: The fans should be oriented to move the air in one direction from front down low to back and top up high. Excellent choice for a case, by the way.
okay so the fan by the bays would be my intake and the fan on the top left side fan(if you view it from the side) and the top fan would be my outtake.
 
Traditionally the motherboard components needed as much cooling as the cpu. No longer. With that HAF case you can set up a wind tunnel.

Top forward fan position: TY-140. It is a 140mm PWM fan with 120mm screw holes. Block off all other fan positions on top. Get this, or this, or this, and put your PWM fans on it. Plug the power input in a Molex, and the PWM plug into the CPU fan header. That way your fans will speed up when your cpu is loaded, and slow down on idle.

Put your DVD in the bottom 5.25 slot. Use the upper 3 slots for a 120mm or 140mm fan. If the top of the bay is not closed, you can fit a 140mm fan in there. If you bought a PWM splitter with enough branches you can make your front intake into a fan that speeds up when the cpu is loaded . . .

Remove your rear fan. Cut out your rear grill, preferably with a nibbler. Having an empty square in the rear will allow your air to flow silently out the back. No fan needed.

Remove all unused backplane slot covers. That will allow your gpu to breathe.

Remember: air goes where you push it. Left alone, hot air rises, but even the weakest fan can counteract that. If you let your motherboard warm the air that goes into your heatsink you compromise its ability to cool your cpu.
 
. . . Remember: air goes where you push it . . .

Or, where you pull it.

Having said that, I like to work with nature, not against it, whenever possible. I like to take advantage of the fact that hot air wants to rise.

You want to be careful in placing fans so as to cool "hot spots" that you don't unduly disrupt the overall air flow pattern and cause other problems.

One advantage of the HAF 912 is that it has fans in the top panel so you can use air coolers that mount only north and south, which is true of some of the best ones, and not lose cooling efficiency.
 
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Overall, I'd try that side panel fan as both intake and exhaust, and compare gpu temps as well as cpu temps. With the slot covers removed on the backplane (with a nibbler in hand you might also be tempted to remove the slot pillars -- the sheet metal strips between the slots -- as well to free up more air; I did) and with the rear grill removed, you can have all your fans set to intake.

The value of an all-intake setup is that your air comes in only through your fans, which you can filter against dust. The value of a free exit for your air is that you never develop a positive pressure. Positive pressure cases can develop hot spots where the air stagnates. To avoid that you either have to have a balanced intake and exhaust (hard to calculate or measure) or a negative pressure rig (sucks in dust through crevices and deposits it on your components) or cut open the rear so nothing can build up. I prefer the last because it means fewer fans, less noise and no need to calculate intake vs. exhaust.
 
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