There are actually two PWM fan headers. However, the CHA_FAN port only allows for a fixed speed in 10% increments, so I don't use it.
I'm actually running a splitter right now for the 120mm intake and CPU fan on the CPU's PWM port, which has very limited but not entirely unacceptable fan speed presets available. I also replaced my power supply's fan and had run a second splitter off of CPU_FAN for it, but a few days back I got out my soldering iron, added a resistor, and connected it where the power supply's stock fan was attached. Ideally, I'd like to be able to control the chassis fan and CPU fan independently, as CPU load isn't always high when my video card needs air.
I was looking at the NZXT Grid+ as a possible solution, and it appears to be cheaper than the Aquaero 5, as well as not requiring a 5 1/2" bay.