OK, now I understand what you have and how it is intended to work. I hope!
I think you have a side fan that has two wire sets coming out of it. One probably has two wires only (red and black?) to a 4-pin male (pins sticking out) Molex connector. The other probably has three wires (red, black and yellow) with a much smaller female (three holes) connector that fits onto the SYS_FAN pinout on a mobo. I misunderstood about your fan's "controller" - there is no separate controller module with this fan. The only stand-alone controller unit you have is the extra Zalman Fan Mate 2 you bought.
The two sets of wires coming out of the fan are ALTERNATIVES. You do NOT connect them both! You have a choice to make. The "best" alternative is to connect it to the mobo SYS_FAN pinout only using the small 3-pin connector and wires, and leave the Molex connector unused. In this case you do NOT connect any extra Fan Controller module anywhere. With normal mobo functions working, this provides power to the fan on the red and black leads, and a fan speed signal back to the mobo on the yellow lead. Within the BIOS the fan speed is read from the yellow wire and displayed for you in certain places. Also in the BIOS you have a few choices on how the fan speed is controlled. The simplest is no control - just run full speed at all times. The one more commonly used is to let the BIOS control the fan speed by changing the voltage supplied to the red wire.The BIOS uses an actual temperature measurement from a sensor on its mobo to decide what speed the fan should run. A few BIOS's also offer a third alternative that you can set the fan to a fixed speed less than full speed.
You should try this setup first to see whether it works. I realize that you believe it will not because the SYS_FAN output port on the mobo is "fried". If you are right, you will prove that to yourself quickly by hooking it up right and trying to run the fan from that pinout with various BIOS settings for fan speed control.
If you verify that the SYS_FAN pinout on your mobo is not working and can't be used, the next thing to check is whether there is another. Some mobo's actually have two (slightly different) SYS_FAN pinouts on them. If yours does, try it. There's always the possibility it also was "fried", but it might work. However, some mobo's with second SYS_FAN pinouts do NOT use automatic control on them, so you don't get the speed control you want. IF that actually does drive your fan at full speed all the time, though, you have the solution with you. You can insert the Zalman Fan Mate 2 unit into the line from this second SYS_FAN pinout to the fan and use it to set a fan speed slower than full.
If that does not work, or you don't even have a second mobo pinout to use, you go the the other alternative. Disconnect the 3-pin lead from fan to mobo pinout and curl it up out of the way. Instead use the fan wires with the male Molex connector to plug into any of the standard female Molex power supplies. This should get your fan running full speed at all times. No amount of connecting things to your mobo or manipulating BIOS settings will change that.
The ONLY way to change (reduce) the fan speed fed from a Molex connector is to insert a Fan Controller unit into the feed wires. The Fan Controller must plug into the female Molex coming from the PSU, and then the fan must plug into the controller output wires. Now in your case we have a problem of connectors. I believe the Zalman Fan Mate 2 has only the small 3-pin connectors on the ends of its wires. You can easily use the one with two (or three?) PINS on it to connect to the 3-pin small connector coming from your fan - the one that you previously plugged into the mobo pinout. That gets the power from controller to fan. What is missing is how to connect the controller to the Molex female coming from the PSU. For that, we're back to that item I mentioned before - get an adapter from a parts shop designed to let you plug a fan with the small 3-pin connector into a 4-pin female Molex socket. Use this to adapt the Molex connector to the controller's INPUT connector on the end of its wires. This puts the Zalman unit in the line between Molex supply from the PSU and the case fan, and so it can do its control function. If you do this, once again the wire from the fan that ends in a Molex male connector will NOT be connected to anything.