If you want to go a little more in depth than just listening for a nice, even volume during the THX sweep, you can use that test tone "CD" that I mentioned before and a measurement device like the RadioShack SPL meter or just an SPL Meter App for your smart phone
Without a manual EQ of some kind, there won't really be much that you can do about any frequencies that are a bit too high or too low. All you can really do is see how Audyssey has EQ'd your frequency response. But measuring can sometimes be fun...just to know. Also, Audyssey 2EQ isn't exactly very granular in its measurements, so it might still leave quite a few peaks and valleys. That test tone "CD" plays individual 1Hz intervals for a 10 second span at each Hz! So it is very granular and will really demonstrate any frequencies that peak or dip.
If it really bugs you, you can fiddle with placement and phase some more, but there isn't a whole lot that you can do
Bass traps can help to take some of the room's acoustics out of the equation. Most rooms have a handful of really bad frequencies that result in huge peaks or dips, and bass traps can help to quell those.
And an EQ system of some kind can smooth out all of the smaller peaks and maybe some of the small dips. The Behringer Feedback Destroyer is a very popular, quite inexpensive manual EQ, but you can wind up fiddling with that thing until the end of time!
There are also automated EQ systems, like Velodyn's SMS or the SVS SubEQ that uses a higher level of Audyssey. But those cost more than your new sub! Newer receivers with MultEQ XT or MultEQ XT32 also offer a lot more EQ in the bass, so one day, you might decide to upgrade your receiver and just get better bass EQ along with it!
You can see by now that it's easy to go crazy when it comes to bass
Lots of people do. But one really important thing to remember is that humans really don't hear bass very well. We suck pretty bad at hearing bass, actually
So don't go pulling your hair out over one or two peaks or dips in your frequency response, and don't spend all your time trying to find the PERFECT spot for your sub or the PERFECT cross-over with phase PERFECTLY aligned. Unless you listen with your head in a vice, your listening position isn't always exactly the same anyway, so some variances are going to occur!
But if you "Crawl for bass", let Audyssey do its thing, and confirm the setup with the THX bass sweep, you should have a pretty darn good bass setup! Nice and even, seemless handoff between speakers and sub, and maybe a little "goosed" output for some really spine-tingling, gut-rumbling movies and games
