Run from instrument to the wah to the amplifier. I sometimes use a boss digital reverb/delay 9hooked up through the effects loop) for recordings. I use the peavey footswitch and use the bright option for the clean channel. I use a PRS custom (mahogany body and neck, maple top) so a Les Paul will sound good through this also. Stay away from single coil guitars when using these settings. When I use my strat it sounds like crap. When using any other effects run them through the effects loop, it sounds a buttload better.
Channel A left volume: 2
Channel B left volume: 4
Channel A right volume/gain: find volume that matches B level
Channel B right volume/gain: 3