That will be a great system, btw! Congrats!
I found your manual...
http://www.energy-speakers.com/images/download/448.aspxLooks like the "x-over" input bypasses the built-in low-pass control. If you are using the Denon to manage the bass (and you probably should), it probably doesn't matter which input you use.
At any rate, I'd use the low level input instead of stringing cables all over the place. Then, you can experiment with various settings and both of those connections to see if there is any useful difference.
