#1
Even though my guitar is in tune. Notes further up the fretboard sound lower then they should. HEEELLLPP!!
What do I do?
I am Nobody, Nobody is perfect. Therefore, I am perfect
#2
it's your intonation.

You know those metal parts in the bridge that hold your strings? You have to move those forward (with a flat or Phillips head) until the intonation is correct within your tuning.
#3
Do I just keep changing it until it sounds right?
Or is there a way to tell through harmonics or something of the sort.
I am Nobody, Nobody is perfect. Therefore, I am perfect
#4
the note should be in tune to the strings tuning at the 12th fret.
#6
Long T's link is really cool. The only thing I would add is. When adjusting the set up between wound and non-wound strings (D+G) there will probably be a step in the distance. I tried to set up a Strat a while back and the step was far greater than I first thought it would be. This made for a lot of dickin' around. I eventually took it to a luthier. AUS$60.00 full set up. Worth it.
#7
Sweet. This helps a lot, thanks.
I am Nobody, Nobody is perfect. Therefore, I am perfect