Hi, this weekend I bought a Fractal Design Define R4 and lifted over all my gear into it. The image below shows my current fan layout.

The motherboard is an Asus Z68-V GEN3.
- Upper drive cage is removed to improve front air intake.
- Fans A and B are the 14 cm 3 pin fans that were included in the case. I put them at 7 V since I can hear them at 12 V, but not at 5 or 7 V.
- Fan C is the default Cooler Master Hyper 212 EVO fan, in a push configuration. It is connected to CPU FAN header.
- Fan D is a Xigmatek XAF 14 cm 4 pin PWM fan. It is connected via a 3-way+Molex splitter and is synced to the CPU fan. (With the current setup I could get the same effect by connecting it to the CPU OPT header, but with fewer cables involved so I might do just that.)
- Fans E and F are identical to Fan D. Fan D is connected to CHA1, which is a 4 pin non-PWM header (I think it is voltage controlled, definitely not PWM).
- Fan F is connected to CHA2, which is a 3 pin slave of CHA1, so the E & F are always giving the same RPM. I cannot control CHA2 directly, but it must be controlled by CHA1.
- There is a side mount and a forward top mount that are not used and has the noise blockers covering the ports.
For the GPU I am using EVGA Precision X, and I am using Asus Fan Xpert 2 to set up a fan profile for the CPU fan and that works effortlessly! The processsor is a i5-2500 at 4.3 GHz. With E&F off I am getting CPU temps of about 45 C in Intel Burn test, and below 40 C in games, which I find quite remarkable, so I really do not need more cooling for the CPU. However the GPU temps are worse, and since I want to replace my old card any day now with an overclocked 7950 that area needs some attention. Also the GPU noise is the loudest of the entire case so keeping the GPU well supplied with cold air is a priority. The idea is to supply the GPU with cold air from F and pulling it out at D&E.
The problem: Fan Xpert 2 cannot create a fan profile as a function of GPU temp, or anything else but CPU temp for that matter. Instead I have E&F synced to CPU temp, where they kick in at 40 C, but since the CPU is so cool that never happens in a real life situation no matter how hot the GPU is. I can set the CHA1 threshold lower than 40 C to make sure they are almost always spinning at low speed, but that is pretty stupid solution since they wont spin up with increasing GPU temp.
Before you suggest it, I have tried Speedfan and it does not report CPU temperature(!), and the individual core temps look completely crazy. That, and that it would not let me actually control the speed of any fan makes me think it is just too far outdated and does not support newer motherboards.
Is there a way to control fans E&F through Fan Xpert 2 or any other software? If that software also can control the GPU fan that would be a very nice bonus!