How about this.. I currently have 2x120mm 2500RPM fans, 1x140mm 1800rpm fan, and 3x230mm fans that run about 1400 rpm. All which are ran from two fan controllers on the front of my case. With them turned all the way down the only noises I hear are random reads from the HDD's and the sound of my Antec PSU. At full tilt, the 2x120mm fans running at 2500RPM sound like Learjet getting ready for take off under my desk.
you should have gotten some fans with your raystorm 240 kit but you could still choose aftermarket fans to go onto the rads. The stock bitfenix fans can also be swapped out but that is totally upto you. Though I have no idea of the fans that come with the case to be operable via 3~4 pin mobo/fan header. Push+pull on a rad will yield better temps more noise and will subject you to getting a fan controller.
Can I use the fan controller to control the pump speed of the Raystorm?
If I've got this right, you have the 750L pump version of the raystorm kit, which means this the first of the raystorm kits released(and concocted by re-sellers to help sell their already lying around rasa 750 kits). Thus it'll be directly plugged into the psu and has no way of pump speed option, unless you have the D5 which should have a knob on the back of pump to adjust speed from 1 to 5.
What are the benefits of using a fan controller with regards to silencing my system as much as possible?
you can't really silence anything in terms of fans. Its a motor with blades that cut into the air and pushing it behind the frame. Anything that cuts into the air will produce a swish sound. You may be able to quiet down the fan but it wont be silenced. for that you have sound dampening foam to line the case - but the airflow will be hampered thus the temps will go bad, unless you have a rad externally mounted drawing cooler air then again internal components will get hot again.
Even If you get your fans to run at the absolutely bottomed out motor speed, most fans have an audible tick - while others don't notice them.
You could look into the lamptron 8 channel fan controller or the bitfenix recon.