You should still be able to calibrate using Audyssey for a 2-speaker setup. There isn't any special setting for that, as long as you set it up properly in the speaker setup the Denon will "know" that you only have 2 speakers and downmix everything to stereo. If you look on the display, on the left it will show you what channels are being received, and on the right it will show you what is being output, so you can see the downmix.
I run 3.1, used to run 2.1. I would just leave it on "Standard" for whatever surround sound input you are listening to. i.e. if you are watching a 5.1 DD tv broadcast, just hit "Standard" and put it in standard Dolby Digital mode, and it will automatically downmix. If you are listening to a blu ray from PS3, just hit "Standard" and it should say "MULTI CH IN" and then downmix to 2 channels. You can also set up your devices to just output 2-channel PCM, but I'd rather let a sophisticated $1000+ AV receiver do the downmixing than a cable box.
If you are listening to 2-channel native content (CD's/music/standard cable), just put it in Direct or Stereo mode.