1) I would go with the front and sides as intakes and the back and top as exhaust.
2) With many (if not most) motherboards, the answer is yes. My Gigabyte board could auto-detect that the fan was a three-pin and control it with voltage, but there may be boards that require you to manually "tell" it what kind of fan you have plugged into the CPU fan header. (I used 4-pin fans for my Asus, so I never tested the 3 vs 4 pin question with it)
My Gigabyte referred to the different control methods as "PWM" (4-pin) and "voltage" (3-pin)