Controlling fans with your motherboard can be tricky - sometimes it works great, other times not so great. Generally, when we're doing water cooling - this adds more than the typical amount of fans to the system, making it impractical to hook radiator fans to the motherboard. If you don't have a fan controller, you'll want to hook your extra fans up directly to your PSU. Again - it depends on your motherboard - maybe you have enough connectors, and maybe you'll have control capabilities. BUT (and this is just my opinion) - I think it's cleaner and safer to leave the majority of fans off the motherboard, and I wouldn't recommend piggy backing fans on any one header on the board.
Fan controllers are cheap - and give you flexibility, but they are not a necessity.
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