Holes down - always!!!!!! You are maintaining a hole through the dirt, you want the water to enter the hole as soon as possible. You do NOT want to have a pipe full of water. The idea is to move the water to somewhere else, not to let it into the soil/gravel. The sock and/or gravel is to try to keep dirt from choking the holes. Ground cloth on top of the gravel is to try to keep the gravel from getting choked.
Most of the crinkle wall (my term) black plastic product is done with slots all around the pipe.