I did run Audyssey, but I've been reading that it might not calculate the phase of the subwoofer correctly. I was reading about it on the Rythmik site but it was a little confusing to me. Does Audyssey do eq changes also?
You'd have to be more specific about Rythmik's piece, link it. Audyssey does a decent job I think of matching the phase with the speakers for as simple a setup as it is. What gear would you provide to implement further tweaking should the calibrator need such? Not much you can do to program the Denon outside of the Audyssey app, which you could do as well (are you using the app?).
Yes, Audyssey does implement an eq scheme if you ran it, but you can turn it off (and leave level/delays in place) easily enough, or use the different curves (Reference vs Flat....aka movies vs music). Some avrs have the Audyssey bypass L/R feature (where it does not eq the L/R speakers, but not really an Audyssey feature). There is further dsp sometimes enabled by running Audyssey like Dynamic Volume (I turn that off), and a further change to eq called Dynamic EQ (more a loudness contour for less than reference levels, also tweaked by another setting called Reference Level Offset). So a variety of ways you can go with eq, or not.