Should I set my settings (high,mid,lo) to match my pedal(such as the EHX Metal Muff) or set them all to middle?
Such as: (on the pedal)
Then what should the amp be set to?
I always match my pedal to amp, so when going from clean to dist there is no significant difference with the tone

Epi Les Paul Std w/Duncans
Cry Baby From Hell
Marshall JH-1
EHX Metal Muff
MXR EVH Phase 90
Carl Martin Classic Chorus
EHX #1 Echo
Ibanez LU-20
Dunlop DCB-10
Crate V50112
Tascam US144

I'd say just mess around with your amp's eq setting to see how close you can get, if you match them you might not get enough treble with both at three and it will sound muddy. I usually just plug into my amp, get the eq settings i like, then plug in pedals and set them and it works for me.
I'd set your amps eq until you like your clean sound, then plug in your pedals and set them until you like your tone with them...
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