Two different bikes. Madone will be more "racey". More aggressive riding position, shorter wheelbase, more nimble, or twitchy feeling depending on your preferences. Domane will ride smoother, more relaxed riding position, longer wheelbase, more stable feeling.
Equal spec? Get the Madone for $1k less. I've ridden both, the Domane is excellent but expect a stable, more relaxed feel. It's still as stiff as anything you'll find everywhere it counts.
The Madone is more responsive due to it's more standard geometry but Madones/Treks have never been twitchy. It also has excellent compliant ride quality, just not as smooth as a Domane with the de-coupler thingy.
Both great bikes the the Madone is a great deal that won't leave you wanting for more.
I assume both had Ultegra. $3300 seems like a good deal. Madone is a very proven bike.
The Domane has an interesting design and seems cool. I'm sure it's just me but the name Domane sounds girly to me.