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So I have three fans now and what would be the best fan config for 3 fans in my case? also is it bad i have my hdd mounted like that?

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2 in the front, 1 out the back is all that's necessary for most systems. If you feel you need more exhaust then add one to the top rear most spot.

 

As for the HDD, I don't see any issue. You can get a good 5.25-3.5" adapter that would make it look less ghetto for $10-15.

 

Add some black zip ties and a black 24 pin extension and you'll have a very nice little system.

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My personal preference is two AF intakes since there's just such a gap between the front and the actual components that there's not really a reason to run exhaust. And then as many SP or AF fans from the back top any bottom as you can fit. Move the hot air away immediately and flow the cool air in.

 

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Move one of the front fans to the back for exhaust and flip the other fan to be an intake instead of exhaust. 

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If you have 3 case fans, 2 front intake and 1 rear exhaust is best config. At the moment your front fans are exhausting. So first thing would be to flip them other way. Fans have arrows on frame to show direction of airflow. If not, all fans blow towards frame side.

As for HDD, its fine. You could get adapter or even anti-vibration mounts. But its fine. I wouldn't move case much around though.

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