Both.
If you hook them up with your mobo, then you can monitor them through HWMonitor or any type of monitoring tool.
The only thing I don't like about hooking fans via Molex is that it's a pain in the @$$ to take off if you have a crappy power supply with no assists to help you push them off.
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“Wise men speak because they have something to say; Fools because they have to say something.”
-Plato
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