My use is very quiet for work and Internet, and high airflow for gaming for hours.
1. Some motherboards are better than others when it comes to fan control. Asus are probably the best because you would normally get both a choice of fan profiles and the ability to set a manual profile in the BIOS. For most people the Silent profile could be enough. But with the manual profile you could set the fans to the speeds you wanted at idle and at load.
If the Asus BIOS controls are not enough, then Fan Xpert offers more options if necessary. With gamers it is quite common to set up a PWM fan chain of either CPU plus exhaust, or CPU, exhaust and intake. This would give thermal control of case airflow rather than just CPU cooling. Existing case fans can be deployed to other positions, and could be plugged into the motherboard chassis fan headers. Asus motherboards typically give you a choice of fan profiles in the BIOS for the chassis fans as well, and also a manual profile, with again the additional flexibility from Fan Xpert if required.
2. A PWM fan can be turned off if its duty cycle can be set to 0% and 0%=0 rpm. Many fan manufactures set 20% or 30% as a minimum and even this may correspond to something like half the fan's nominal speed. But if you really do want 0% duty cycle=0 rpm then the recently introduced Noctua PWM fans will do this. I am not sure if turning a fan off is really necessary, the Noctuas for example would be extremely quiet at their normal minimum of around 300 rpm. But Asus motherboards do allow a minimum PWM duty cycle setting of 0% for the CPU in the BIOS manual profile, so you could set up a semi-passive profile where the fans were off until a set temperature was reached.
3. Bottom fans help because they supply air directly into the GPU intake area. Having said that, on the 550D the intake fans can be mounted on the drive cages and would then supply air directly in the same way, but would be pulling it over any hard drives which might make a difference to intake air temps.