Oh. Information I found online about your board only shows the 3 total connectors - possibly the rev 1.1 added the additional headers.
The difference between 4-pin and 3-pin fans are that 3-pin fans can only be controlled by changing the voltage applied to the fan, while 4-pin fans are controlled using Pulse Wave Modulation. Basically they turn on and off really fast, and the distance between the intervals controls the speed. Whether the motherboard can handle both, or just PWM fans is a question the manual *should* be able to answer, though from what it looks like the motherboard can only do PWM, if the exhaust fan running full-tilt is any indication. There *might* be an adjustment in the BIOS somewhere, again, couldn't hurt to look.
Most separate fan controllers, at least ones I've seen, use voltage adjustment to control the fans, and as such it would be able to control the exhaust fan. As for brands, I've been using single-channel internal controllers on my system, so I'm not as up to date on current front panel controllers.
EDIT: After taking a look through the manual, from the pin layout on the headers, SYSFAN_1 has the ability to control by Voltage, and 2/3 only can control by PWM control (4-pin fans with speed control). 4 is only for full speed, no speed control.