I'm not sure whether there's a "right" way, but the way I've always done it is, guitar preamp first, then EQ pedal, then EQ on the mixer.
Your setup is slightly different since you're using an amp. Perhaps some amp users will chime in with their experience...
If I were using an amp, I think I'd actually pre-set my amp EQ first, then the guitar preamp EQ, and fine tune with the EQ pedal. In my eyes, an amp does more to shape tone than a PA mixer since the amp is specifically designed for a particular instrument/input source.
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As my username suggests, huge fan of Yamaha products. Own many acoustic-electric models from 2009-present and a couple electric. Lots of PA too.
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