For me, both the X and Y axis movements were reversed in Pronterface and Repetier-Host. I eventually got annoyed by it and swapped the motor directions (by rotating the motor plugs on RAMPS by 180 degrees) and by moving the endstop switch locations to the opposite ends of the travel. I'm pretty sure you can deal with all this in firmware changes, but I wasn't ready to jump into modifying the firmware at the time.

I've had the hex hot end fan pulling air from day one. It helps with ABS prints by reducing airflow pushing down on the print below the extruder.