The mobo controls the fans...if you have them plugged into the board. If they are simply plugged directly into the psu (only have power to them) then there is no control. Plug them into the designated spots on your mobo (Sys Fan 1, Sys Fan 2, etc.) then you can control speeds through your bios or software prog on your desktop.
If the fan plugs are 4 prong plugs for IDE devices then you will need a fan controller to run in-line or do what I did with a loud fan was to force the connector in backwards which runs at 5v vs 12v, super quiet.