Assuming both fans are plugged into matching fan headers (4 pin into 4 pin, 3 pin into 3 pin) then either way may be ok, but you can try flipping it and see if the default speeds are more to your liking. If you've got an ASUS motherboard you can plug 3 pin into 4 pin as well. The way to control them (and the amount of control you have over them) depends a bit on your motherboard, but sometimes there is a utility in your BIOS, or a utility that came with your motherboard (or from the manufacturer's site). There are also third party applications for controlling fan speeds like "speedfan".