I can't get good solid base out of the system
Matt,
Wow! You generated a lot of response and a lot of information. Some of it is hard for my simple mind to follow. This is what I understand...
Audyssey is used to
balance your speakers, including subs. To do this, it can raise or lower the volume of each speaker in your AVR, but only by +/- 12dB. So after running Audyssey, if any speaker shows a setting of +/- 12dB, it means Audyssey went to the max of its adjustment capability. You don't know if it's enough, or if Audyssey simply ran out of adjustment capability. If your sub shows -12dB, Audyssey determined it was too loud and turned it down as much as it could.
Now that means your AVR is at its limit to
decrease the volume of your sub. (I know you want it louder, but stay with me. Remember our initial setup is all about balance. Once you set up that initial balance, you can easily adjust whatever you want to your preference.)
So ideally, you want your setup (Audyssey) to have all speakers near +/- 0dB, so you have maximum flexibility to adjust any speaker
up or down as you wish, (up to +/- 12dB). Your sub is the only speaker that has its own volume/gain adjustment on the speaker. Audyssey is telling you the sub is at least 12dB too loud, so you need to turn down the gain on back of your sub by 12dB, and run Audyssey again. Keep repeating that process until Audyssey sets your sub volume at or very near 0dB.
Now your volume is balanced. Your bass is at the level it was intended. (BTW, after Audyssey don't forget to change your speakers to Small, and set your crossover ~80Hz.)
Your AVR has flexibility to easily set the bass where you want it for music, and a different volume for movies. Read the manual. You can set it up so when you select "Stereo", your sub is at whatever level you want. If you like a lot of bass, you can set it so. When you select TV or Movie, you can automatically get a different bass level.
But the point is, if you begin with an accurate and balanced setup w/ Audyssey, you'll know your system is delivering accurate levels. After that, it is all personal preference.