Audioholics needs an article about "How to setup acoustic treatments in your dedicated HT"
I think if you dig into the Audioholics University section, you will find some relevant articles.
I think that you may be missing the gist of the article though. What we have been exposed to, as far as room treatments, was largely based on large room calculation scenarios. Since home theaters are not large when compared to public concert halls these original formulas were based on, we are now starting to question their validity of these calculation in the modern home theater application. This means we must rethink everything including acoustic treatments when addressing our own acoustic issues.
I hate to say it, but the only real reliable way to diagnose room acoustics is in room measurements with equipment capable of very high sampling rates. Not cheap or readily availble to the average sound designer, much less the audio enthusiast.
The only other real solution is to experiment with acoustic panels and place them according to what sounds best to you. You can try the tradional locations like corners and edges or primary reflection points, but as the article pointed out, we may be doing the right things for all the wrong reasons.
This article should be a real eye opener and I hope everyone who reads it walks away with a new found appreciation for the complexities of audio science.