Setting the speakers as "Large" is a design "feature" in the receiver's firmware external to Audyssey. It's a confusion factor in all Denon and Marantz receivers, too. You need to manually set them to "Small". That's just the way it is.
If Audyssey has set all the speakers to -12, it means its volume control is "pegged". Audyssey has set the pre/pro's outputs as low as it can and they're still too high. This also prevents Aydyssey's room equalization algorithm from working as it should. In other words, your external amps (including the subwoofer) have too much gain. If the amps have gain pots on their inputs, you need to turn them down. Similarly, you need to turn down the subwoofer's volume adjustment. If the amps don't have gain adjustments, then you need to get in-line attenuators to reduce the signal that they receive from the pre/pro. Then Audyssey will be able to turn up its output levels and fill in the dips in frequency response that you've noticed.
Marantz SR7009/7.1.4/FH+TM/DefTech PM1000/LCR+TM amped