Almost all CPU fans blow air onto the CPU. Exceptions to this are very rare. You can still feel airflow on the other side of the HSF, though, if that's what's making you think it's the wrong way around? I don't know what HSF you have, but there will probably be little arrows on the fan which indicate the direction of airflow. If it's mounted the wrong way around, just take it off, flip it over, and screw it back in.
As for your restarting problem, what upgrades did you perform? If you replaced the motherboard, you will need to run at least a repair re-installation of windows.