It won't make a big difference. It's just one fan, and intake air on the bottom of the case isn't that hot. But I would switch it around anyway just to separate it from the rest of the case airflow. I like having a traditional front-low to rear-top airflow. Also, PSUs typically have the cables protruding from the side that will be closer to the motherboard tray when the fan is facing down.
Of course, if you don't clean your floor from dust very often, it'll could get dusty inside. The bottom mesh does have a filter on it, right?