I'm thinking of getting a EHX Metal Muff and I'm wondering how well it would work with a Roland Cube30x. Would I run it through the clean channel?
It would work fine, run it through whatever channel you want.

Fender Deluxe Players Strat > Big Muff > LPB-1 > Moog Ring Mod > MXR Dynacomp > MXR Phase 90 '74 > Fender Hot Rod 410 (soon)
it would sound best through a clean channel

i find that my roland cube 60 has enough gain as it is

wait till you get a tube/valve amp and then get a pedal
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Axe Fx Owner