well according ot some of the folks here the "correct" way or rather the way they was intended to be mounted is
with the dust cover under the panel..
but i seen VERY few machines setup like this, even brand new dedicated games usually had it mounted on top.
so while some say the correct way is under. the fact of the matter is the usual method was on top.
this is gonna be a personal choice for you, personally i think i prefer mine on top.