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)
You want to have an air flow inside the case and with your choice there would not be a flow. You need to set the fans as Zinonly suggested.
If you look closely at the fan headers on the motherboard the four pin ones especialy you'll notice that the flat plastic piece is more to one side and that is to accomodate a three pin connector. So the four pin connectors on the motherboard are designed to have a three pin connector plugged into it.