I have just bought a Cosair H100i to cool my CPU but I placed the fans were they exhaust air from the case, now the manual says that for optimal performance I need to place the fans to were they suck air in. Does this matter?
Not overly, I recommend leaving them in exhaust.
Having it set up as an intake would mean that it would be trying to push hot air down, while also dumping that heat back into the case. While this wont affect your CPU temps much, it will have an impact on motherboard VRM and GPU temperatures.