For both bottom and top mount the fan should be sucking air from the bottom and blowing out the back.
Bottom mount is better for this because a bottom mount will suck fresh clean air from the vent/filter in bottom of case, while a top mount will suck the already hot air from your CPU cooler and parts to use as "intake air" to cool the power supply.
Mounting the fan the opposite on a bottom mount wont immediately cause any problems but it is disruptive to the natural airflow of the case and could cause heat issues, especially on an overclocked PC that is putting a thermal load on the CPU cooler to begin with.