Plug your guitar into the main input on your amplifier and turn the amp on.
Turn on any foot pedals or distortion that you'll be using during the EQ adjustment process. If you're only going to be using clean, or switching back and forth between clean and distortion, then leave your amp on "clean" for now.
Play a chord and let it ring out. Turn all of the amp EQ knobs all the way down. In other words, set your "low," "mid" and "high" knobs to zero. There shouldn't be any sound coming out of the amp right now.
Keep strumming chords and turn up the "low" knob to at least halfway. Bring in your "mid" and "high" knobs slowly to tweak the EQ even more. If you get the right tone, but feel like the volume is too low, simply increase the "master" volume knob.
Turn on your distortion pedals once you've found your "clean" tone.
Adjust the EQ knobs on your distortion pedal, much in the same way you did for your amp. Begin by turning all of the EQs down to zero. Bring in the "low" tone first, followed by the "mid" and then "high." Once you get the tone you want, adjust the "master volume" knob/switch on your pedal so there's not a huge difference in volume between clean and distortion.