My case has 3/4 molex connectors on the fans included with the case. Do I need to get adapters for some of them, or will they all fit into the motherboard?
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They will fit into the molex from the PSU. If you want to connect to the motherboard you will have to use fan connectors. The fans can share a molex if you want since there is very little load from each fan.
Should I just connect them with the power supply? Or do most people connect them to the motherboard?