<font color='#000000'>Room size and what your floor are made out of play a large part in the decision. Generally, for a down-firing subwoofer you'll want hardwood floors or some other hard surface for best response.
Side firing subwoofers will do better in a smaller room (as opposed to the same size down-firing in a larger room) and is forgiving on what your room/floor is made out of.
All of these generalizations assume that both subwoofers are of demonstrably "equal" quality. Otherwise, a bad quality sub of either type will be outdone by the other.
There's much more than this - but until you provide some more details maybe this will whet your apetite...
[Edit: Just ONCE I'd like to post without spelling errors...]
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