HWMonitor won't show any fan speeds because there is no return to the motherboard, the fans are fed from the psu and controlled by the switch. If you want to have bios or software control of the fans you'd need to attach them directly to the motherboard. As for the CPU fan, 'standard' means it will ramp up to a faster speed than 'quiet' and do so at a faster rate. The bios does not care about your temps, it only cares about its temps and this is probably why you are getting what I believe to be higher than usual temps from that cooler. At anything under 70C, the bios is not going to use 100% max duty cycle, its only going to ramp up to what it needs in order to maintain less than 70C.
So, you can change this in the bios, either set it to 'performance' or 'extreme' or whatever the top ranks is, or actually manually change the duty cycle to set a minimum of say 60% (that's about 60% of the speed your fans are capable of) and max duty cycle temp, say 50C, so if and when your cpu reaches 50C, the fans ramp up to 100%. That's whats called 'setting a fan curve', you are manually stating the boundries. There is more than a few software programs that will do this for you, and have nice little graphs and pictures etc that you run through Windows. Asus has Fan Xpert, MSi has Core Center etc. Whatever your motherboard is, it will have a utility such as this. I'd also recommend you put the fans on the mobo too, having them auto monitored and controlled to keep case temps down I believe is better than doing it manually. You can also set fan curves for them too, so all is cool and quiet when idle but will ramp up when the cpu is very active.
As far as noise is concerned, the case will dampen most of it, but if you can live with a few extra degrees of heat, you'll be able to turn the fans down a little.
Yes. Point the cpu fan exhaust towards the back, that is correct. The 120mm fan takes cool air, blows it through the first bank of fins, where the 140mm fan picks it up and sends it through the second bank of fins and then the case rear exhaust picks it up and shoves it out the back.
Basically, 'standard' is doing you an injustice, you really need to take control of all your fans and optimize them for your tastes, not so much the cpu's requirements