The fan at the rear of your case is always supposed to blow hot air out of the case, just like the fans on top of your case. Intake fans are most likely to be positioned at the front, at the sidepanel and at the bottom of your case.
This is how it is mostly done, but if you can give the type of chassis you have I can look it up.
Those fan controllers do exist. Take a look at Scythe. However I would not shut down any fans. If they make noise, just slow them down, and before buying a fan controller, check your bios. Most of them a fan speed control page in it, mostly situated under the Power tab.
Yeah, if you need to slow down just one fan, you can buy variable resistor with all the plugs on it you need to connect your fan to. You can then build the potentiometer into a small box or something like that and make your own fancontroller. It's cheaper then buying one which has all sorts of gadgets like RPM displays (your mobo can do that too) and LED's to tell you stuff you're not interested in.