If you have a normal box (e.g. 6AL) with no knobs or buttons, then under the passenger seat is a perfect place for it. No heat, less vibration, out of the way, and so on. I've put it there on several of my mustangs over the years and it's like it was made for it.
Some people like to have their MSD box showing, but I don't care - so I just leave it where it is.