You can orient the cooler in any direction you want. Generally this will be blowing up or blowing back.
My case, the Silverstone TJ09, mounts the PSU on the bottom and the CPU is very near the top. I have two 120mm fans in the top of the case blowing air out, so it made sense to align the cooler that way... there is also theories on the alignment of the pipes and the cores inside the CPU... but it's not proven and there are some indications it's not even an issue.
Most people who have P5Qs do not have issues with Crysis. Some few do, such as me.
I had to contact Securom, the company that handles the security software for Crysis. They provided me with a new crysis.exe and that resolved my issues. They never told me why I got the emulation software detected error, but I guess it's P5Q related, although not common.