Pies,
The Scythe fan controller you linked to WILL NOT work. It has the same three-pin fan plugs as your motherboard apparently does. What you're looking for is a fan controller which lists at least one PWM fan control in its specs.
For about $7, you should be able to get another FanMate2. They're nice and cheap like that. I managed to crack the case on mine when transferring it to me new chassis (the double-sided tape is amazingly sticky), and the circuit board inside broke. Tape, apparently, is mightier than circuits
. Check to make sure the new one comes with all the cabling you need. Otherwise, you should be able to get what you need from FrozenCPU.com.