If the fans have RPM sensors on them, you might want to hook them up to the motherboard for an extra eye on your system. Use MBM then to monitor the fan speeds. Plus, the system could be able to control the speed of the fans depending on the temp of the case. I believe plugging them into the fan connectors on the power supply will control the speed of them also, that is, depending if your supply supports this feature. I for one would have my case fans plugged into the motherboard if I weren't crunching DC units and have them plugged into a baybus. Either way, it's your call.