One thing I would add. If the amp for the built-in subs don't have gain control, you should turn the speaker channel level for the subs to -12.0 on the Denon before starting. You can always turn it up later.
If you need to further decrease sub volume, you can manually increase all the other speaker channel levels by 5.0dB to 80dB, instead of the usual 75dB. Audyssey will set to 75dB. Just increase each channel level by 5.0dB, but keep the subs level to -12.0 when starting. This way, your MASTER volume will be lower (thus the Sub volume will be lower).