so i want it professionally done (already wasted $58 at a store, when i got it the intonation was terrible). for know im just adjusting the intonation. my question is why after correcting my intonation does it get worse?
It's it possible that the store didn't work on the guitar at all? Mistakenly missed it?

Otherwise if it's worse after fixing it it's because you're doing it wrong..
And no, Guitar Hero will not help. Even on expert. Really.