I personally would leave the stock fans connected to the fan controller for manual control. Meanwhile the fan you added would be connected to the Motherboard to be controlled by software
That sounds good. The mobo has three fan inputs plus a CPU fan input. I'll use one input for the non-stock front case fan (antec), then that leaves me two other fans inputs. I don't actually have the vid card in my possession yet, but expect it in the mail soon. I suppose I could use the second fan input for the GPU fan. If I do, I'll still have one extra fan input. If I don't use it for the GPU, then I'll have two extra. In that case, might it be better to put the fans into the mobo instead of using the Fractal Case fan 3 speed control?
As you say, I'll plug the Antec TrueQuiet 140 into the motherboard. This fan has its own two speed control:
800 rpm @ 0.10 A
500 rpm @ 0.04 A
Is it fair to say I should set the fan to the higher 800 rpm setting and then control it with the mobo bios or other software?
Also, is there an opinion on whether or not I should keep the extra 5-bay frame in place? Seems to me I should just remove it.
I have an SSD which I expect to mount in one of the lower 3 bays. I'll put the HDD on top (for best exposure to the fan), then next install the SSD and then leave the last bank empty. The R4 also has an option for installing the SSD behind the mother board. I can do either, so I guess I'll just use the bay. Not sure if SSDs get warm, but it would seem behind the mobo is a great place to overheat.