Audyssey will do the "room correction" for your speaker set up. It will set up what "it" thinks is best given the test (pink noise test) it receives back. I may stand corrected here but I do believe it will only do the speakers itself and not the sub as you will have to set/tweak that yourself. Once Audyssey is ran... you will/may still have to "tweak" the settings to your likeing ( you will just have to get use to it is all... and judge for your ears!)
Anyhow.... to answer your first question, the Audyssey has nothing to do with what you are reffering about, the low volume differance that is. Here is a simple fix for your question/problem:
*Just run Audyssey first to get that out of the way thou.
*This is off your Onkyo remote that is
1) Press "home" as it will get you to the on-screen menu
2) Select "audio" by pressing enter
3) Arrow down to where is says "Dynamic EQ"
4) Turn on Dynamic EQ
5) Arrow one more down to Dynamic Volume & arrow right to where its on and switch to "light"
Actually, the sub is also calibrated by audyssey. What audyssey does (besides other things) is set the distance and level for each speaker so they reach the same "volume" at the hearing position. This could affect the overall volume you're getting. Try audyssey and see if that makes it better
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