I have mounted them every which way, and everywhere for guys who have had ideas of ways to hide it. Upside, downside, rightside, leftside, no difference, put it where you want it. if it gets wet enough to bother it one way, it would any way you mounted it anyway.
That being said, every so often you get one that is noisy, not sure why, but if it's inside the passenger compartment you may not be happy.
I personally prefer under the hood, although I did hide my Accel Annihilator box under my batter tray on my Mustang, if I ever put one on the truck it'll be right on the inner fender