Hi Sam,
I have the Elite 56txi, and I have kept my mains at large even though I have a sub. In fact, since my center and surrounds can supply excellent base, I have them all set as large, and just use the subwoofer at 60Hz and below to help fill in the low range. To do this on my receiver, my sub is set to the "plus" setting in the Speaker setup. I think it sounds great. I'm not sure how well the Klipsch mains handle bass, but if they do a decent job, I see no reason to set them to small.
As for the second question, turning up the channel levels on your speakers should not hurt sound quallity. If doing so introduces brightness, then that is probably just magnifying weaknesses in your speakers. As long as you keep the channel levels balanced, then turning them up should not hurt surround effects either.
