Is it better to hook case fans to motherboard or to simply connect them to the PSU?
Usually hooking the fans to the motherboard will let you monitor fanspeeds in your bios. Some you can adjust the speed also.
If you connect them to psu they will run full speed.
It depends on the fan. High powered fans like the Vantec Tornado series really need to be connected to straight 12V, as they are finicky about speed control and don't even like fan controllers. For normal (low powered) fans, the motherboard is fine as it does a better job eliminating wire mess plus many boards can control speeds on some or all fan headers.
There is no preferred place to plug it in. Just make sure it is plugged in.
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