I placed mine on top. I considered placing it on bottom just to see how that would work out, but I didn't feel like going through with the two steps involved (moving it, and then telling the Wii that it's below). Besides, I like the way it looks.
I recently got some pseudodrapes in my room so it's always fairly dark in there (and actually better for playing in the day because at night, if that blue LED on the remote is shining in a room with no other light besides the TV, that's death in the corner of your eye, and if you have the light on, there IS a glare, and it IS horrible)