Getting your guitar to be perfectly in tune from 1 fret to 12 fret?

I didn't pay much for my guitar so I don't know if that is part of the problem but my bottom two strings the B and high E sound ok all the way up to the ninth fret then the notes start to sound flatter and flatter. I keep messin around with the back part with a screwdriver( my teacher showed me how to tune it by holding down on the twelth string and then making the harmonic ring out to see if the not is correct) but I can never seem to get the tone perfect like the other strings. I know it is time to get a new and better guitar I have warn down my frets so much that it buzzes when I bend in certain spots but I have no job and I have my acoustic which is pretty new. I just want to know if there are any tricks to fixing these problems? What I usual do is try to compromise by tunning just a little sharp so the front is a little out of tune and the back is not as flat. ( playing the paino has given me a more critical ear on how notes should sound) I don't know if I shouldn't worry about it