I can try to answer your first question lol I found a video on YouTube about the pan knob trick and basically from the factory line 6 has the pan knobs panned hard left and right im not sure why but when I make a patch if I pan them both back to unity it seems to effect the tone, kinda makes it more punchy so if I like that sounds for that setting I'll leave it that way lol the only reason I think it comes set the way it does is for true stereo sound for like a ping pong delay.
And for your second question I haven't really noticed the amps being real dark but I think I know what your talking about, usually I set up a parametric eq at the vary end of the chain just so my sound can cut through. I play a strat mostly so of course I downloaded Lincoln Brewster's patches and on his main tone I wrote his settings down for his eq settings and I apply that to most all my live patches. He actually is a studio engineer and he hd500 tone is phenomenal lol but thats player preference.
As far as live playing I get the the best tone I can get at home as close to stage volume as possible without the police being called lol
Then when we practice at church at stage volume I can tweak my tone from there. Bass mid and treble sound way different at louder volumes than at home. Like if you make a good sounding patch at home with just the right amount of bass when you play live that bass setting might be to bassy and over powering.