Audyssey can take a bit of trial and error to setup properly. And depending on the version of Audyssey (MultEQ or MultEQ XT) it can make a *HUGE* difference. I'm not sure what version you have.

I would second the idea about pointing the centers down a bit. You can always prop it up temporarily with a pen or something.

What sub and receiver do you have? It's actually the receiver that decides what should be Large/Full Range or Small. The makers of Audyssey recommend setting the speakers to small if you have an external sub.

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Denon 4520, EPIC80/500/VP180 Speakers