Clean or Dirty; Singlecoil or Buckers?
FWIW, I have the clean channel gain set with a tad of hair around the edges (5-7 depending on which guitar) as I never play "spanky clean," and GEQ assigned to Lead channel only.
So in general, depending on your guitar and pups, start with:
Treb: 5-6
Mid: 4 ...pretty sensitive to change between 2-4, beyond that and you add gain more than mids.
Bass: 5 ...watch it here; this can get flubby really fast
Pres: 6
For Lead Ch:
Gain: 4-7 (depends enormously on how hot your pups are)
Treb: 5
Mid: 3
Bass: 3-4
Pres: 4-5
Tweak knobs here to get close to your tone, but add as little bass knob as possible as this adds lows in the preamp section, making the bottom more loose and flubby. Add bottom in the GEQ as this is a post-preamp tone stack.
GEQ: start flat then:
bass + ~80%
2nd-from rightmost + ~20%
mid fader: flat = more mid definition for classic rock/blues; attenuate slightly here for more "chunk" or "metal" flavor.
Sorry, can't recall the specific freq off top of my head but you get the picture.
Obviously, this is a starting point for which you can tailor to your axe's traits.
Hope this helps a bit.
Edward