Unfortunately there is no streamlined process for parametric equalization. Most of it happens in music recording studios, so we're lucky that there is a computer solution even.
I did not quite understand it at the beginning either, but after reading the guide a few times it became more clear. The goal is to NEUTRALIZE the headphone's frequency response (for exact frequencies at which the headphones sound abnormally loud, you equalize it down, and vise versa), thus allowing it to produce the most natural and high-fidelity sound possible.
Don't bother with bar equalizer (the common ones in e.g. itunes / soundcard settings / etc with like a dozen bars tweaked up and down) because those only boost/depress general frequency RANGES, not pin-point accuracy frequency adjustments, so they do nothing to improve the sound quality of headphones.
It's a long tweaking process - my current EQ file is the result of many hours of tweaking and listening. But it's so worth it because you can experience a constant process of noticeably improving the sound.
