Mine is slightly off stock. .1 mfd coupling caps are .022 instead.
I plug straight into the bright channel, the bright jack. No effects except for *maybe* some light delay every once in a while.
Channel 1 (unused channel) is at about 3'oclock, just before the so-called "mid dip".
Channel 2 (channel I am plugged into) is wherever I feel like it, somewhere between 10'oclock for rehearsal to full on if I really want to rock out and play some AC/DC riffs.
It's very bright, just how I like it, if the guitar tone and volume are full on. I turn down the guitar's volume to go clean, roll off the guitar's tone if it's too bright (like it is sometimes with my strat), and turn the guitar full on for leads.
My 5E3 is running two speaker cabs, a weber ceramic blue dog and a weber alnico 12A150. It goes from a beautiful clean to a nice slightly dirty jazz tone to a marshallesque roar to a nice Eagles lead sound with the twist of a few knobs or swapping of a guitar. All at a tolerable volume. This amp totally rocks! Can't wait to build my next tweed.
For me the only thing channel 1 is good for is sort of a mid control (but it is quite effective at fattening the tone as your turn it up). I never plug into it directly. Never cared for jumpering the channels either, but maybe I'll try it again someday.