You can lay a sub on any of it's sides as long as you don't lay it on the amp or cover up a port. As far a sound quality, there is a so called "breathing room" for a sub but to be honest if your sub is small enough to fit under your tv stand then you don't need to worry about it.
With more specifics of what kind of sub you are talking about then maybe myself or someone else here can elaborate further for you.
