The 3 pin connectors fit quite well on the 4 prong MB connection. You do lose fan speed control, but I just run them on 'high'. They are pretty quiet on those settings, almost silent. They normally come with resistors to make them run slower, those hit the rubbish bin 2nd day I fooled around.
As to direction, they DO have wee arrows on them. Also, the wireing of the fan 'points' in the direction of fan flow, and the fan label is on the output side of the fan. As to direction of flow, that will be a matter of your case setup. Personally, I have both fans facing my rear exhaust fan, no controller, and my cooler is quite quiet.