Hi. I notice in yr diagram for fan speed control you are connecting some of your fans to motherboard fan headers...may I suggest a modification to your setup. You can use 2/3/or 4 way splitter cables in the Commander Pro as long as all the fans don't draw more than 4.5 amps in total..see here for a 3 way. https://rover.ebay.com/rover/0/0/0?mpre=https%3A%2F%2Fwww.ebay.co.uk%2Fulk%2Fitm%2F132480710151
The advantage of doing it this way is that you get RPM read outs of all your fans.. or should I say groups of fans on each fan splitter.. via the Corsair Link software. This is far more convenient for seeing your fan speeds, as you see all your fan speeds in one place on one piece of software. To see the fan speed of the fans connected to the motherboard headers you would require another piece of software to be open on your desktop.
Secondly, by using fan cable splitters you can set up fan curves for each group of fans based on CPU GPU or motherboard temperature sensors.
When connecting fans to a splitter I suggest you only use identical fans in that group as otherwise the commander Pro will get confused about the fan speeds and will not report them correctly and will not control the fan speed correctly. I have 3 Corsair LL120s fans set up on one splitter and they work fine. I have three other fans non pwm so they are voltage controlled 3-pin connector type connected separately to individual channels on the commander Pro... and even though they're not pwm fans the commander Pro controls their speed perfectly. I also have a Corsair H45 cooler fan connected to the commander pro which means I can control the fan speed of that too. You can even connect the pump for the h45 into the commander Pro and it will control the speed of that... but this is not recommended by Corsair as they say it should always run at full speed which is about 4000 RPM... it's a lot quieter at 3000 or two and a half thousand RPM and actually doesn't produce any better cooling after I tested it... also the fan on the h45 doesn't need to go above 1000 RPM because again doesn't produce any more cooling... believe it or not in my pc system at least.
After some fine tuning work with fan curves my case is super quiet yet my AMD FX 3850 CPU does not go above 35 degrees and my ASUS GTX 1060 does not go above 65 degrees even on the heaviest load... for instance running pass mark 3D graphics test and CPU test.
Here is a setup using fan splitter cables. http://forum.corsair.com/v3/showthread.php?t=172785
I hope this helps