For setting up the system correctly, you'll need to have an SPL meter ($35 at Radio Shack)
Enter the Denon setup menu and select the speaker setup.
Here you'll be able to set the speaker type and distances as well as levels and the crossover point (bass management). Set the speaker type (large or small) and distances first (this sets the correct delay times for the speakers) You can set it to read in feet or meters.
Next, set your crossover point for your speakers (you can experiment with this, but generally shoot for within 20 Hz of your +/-3dB point of the smallest speaker you have in the arrangement.)
Finally, do your speaker level calibration. From your LISTENING POSITION start the pink noise level test and set the master volume so that your meter reads 75dB from the left front speaker with the Denon value set to 0dB.
NOTE: Point the meter microphone stright up at the ceiling from the listening position. Hold it at your head level.
Then cycle around all speakers and make them all read the same (75dB on the meter), including the subwoofer. If you have to gain or decrease the sub by more than 3dB - I would get up and use the sub volume control, then go back to the Denon levels and re-tweak.
If you want to check phase and such, and you don't have access to AVIA or some flavor of Video Essentials, grab a THX disc like SW Episode 1 which has the THX optimizer on it (under options from the main menu).
Run the audio stuff in there and you'll be able to check not only left/right speaker phase, but front and surrounds phase as well (to see if your surrounds are in phase with your mains - very important).
I hope I didn't forget anything. I am in the middle oif a cool 5.1 speaker face-off review and saw this post - so I thought I'd answer it quickly.