ive noticed in a few songs, especially the songs with 3 guitars, there is a change in harmony every few notes. Not all the the notes are harmonized together, some ring or just skip a few notes and then continue.

there might be: guitar1 that is the lead harmony

guitar2 that harmonizes with the lead (usually the least amount of notes.)

guitar3 that has seperate rythme (usually the guitar playing the most notes.)

basically its one of those interludes that sound like every guitar is doing there on thing, but still sounds good.
what i want to know is how exactly does that work? how does the harmony change 3rds, then 5ths, for an example, then back again? what is the theory behind that because if its a classical riff then it doesnt really sound as entrict and is somewhat boring.(imo)
I don't quite understand what you're saying, but I do know that in your example, what guitar 1 is playing would be the melody, and guitar 2 is harmonizing with the melody. There was just a thread on here yesterday about the two.
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I think what your describing is a counter melody (or two).

A counter melody is a melody that it a seperate melody from the original melody, and works well as a melody on its own, but combines nicely with the first melody.

To steal a phrase from someone in MT, I don't remember who (please claim it if it's yours):
In a counter melody both melodies work well on their own but when combined make more than their sum.

Basically they both sound good seperately but sound awesome together.

Counter melodies usually differ in rythm from the first melody and don't usually have any one interval apart from the first melody. Counter melodies change the intervals of harmony, often every note. Counter melodies also often tend to do the oposite of what the original melody did, so if the melody is going downwards the counter melody will go up.

Counter melodies almost always differ significantly from the first melody, which stops them just being accompaniment and makes them an entire second melody. This is why it sounds like each guitar is 'doing there own thing'.