The point is to compress only certain parts of the audio. If you have a rhythm guitar where the palm mutes are too loud, you could just throw a normal compressor on, but that would compress both the highs and the lows, and your problem isn't the highs. So put a multiband compressor on, make a band from 50-200 (or wherever you think the problem area lies with the palm mute) and bypass the other bands, and compress it like you would anything else, thinking beforehand about the attack/release/ratio settings. Don't use presets; they're worthless for this kind of thing. Just play around until it sounds good. I've never needed to use a multiband for guitars but I would think that, since palm mutes start off at a normal volume and get louder over a second or two, you'd want a medium attack and a slowish release, so you catch the thumpiness but don't castrate the guitars, and the release will let it fade out like a normal palm mute.
Multibands are really for solving problems in difficult or muddy instruments or vocals. They're great for bass sometimes, definitely for vocals, and occasionally for guitars where the mic'd cab was too thumpy, but if you just want to tighten up your rhythm guitars I would use a normal SSL channel compressor or something. Ola uses the stock Cubase comp in one of his videos and it just adds 1-2db of "glue" by evening out the volume of palm mutes and normal notes.