Drifter, J.B. has given you a lot of excellent info. I'll just add a couple comments. If you've followed the suggested procedure for doing the Audyssey calibration and room correction there's no need to be thinking about "tweaking" the settings(except changing a "large" speaker setting to "small"). Our ears are fine for enjoying music, but they suck for measuring sound differences which Audyssey is designed to calculate.
Also, it'd be better if you dropped the "crank it" terminology. It's hard to know exactly what damaged your woofers, especially since the far more delicate tweeters are usually the drivers which fail, but playing too loud("cranking it")is something that should never be done, for the sake of your hearing as well as your speakers. If you're not able to judge appropriate sound levels you should get the digital SPL meter from Radio Shack to give you realistic numbers to guide you.
