A: What you're describing is the intonation. Here's the trick:
1) First, place the bridge approximately between the points are (or would be, depending on the design) on the F-holes. No, not the curly ends of the holes; I'm talking about the little tips midway along their length).
2) Now re-string it roughly like you had it before (I'm just hoping this wasn't a Bigsby model... that would complicate things).
3) Next tune it up to approximately where the strings should be (i.e., EADGBe). When it sounds like it's in tune and going to stay there...
4) Pick a harmonic on the 12th fret of the high E string.
5) Now pick the note on the 12th fret (same place, but actually fret it this time).
If the notes are exactly the same, then you've got it as good as it's going to get. Odds are this isn't the case, so...
6) If the note you fretted is sharp (i.e,. higher) than the harmonic, then move the bridge a little bit back (You're making the length of the string a little longer). If it's flat, do the reverse.
7) And just to make sure everything is set, do the same thing on the low E. It should be pretty close if you were moving the whole bridge.
8) NEXT TIME... only change one string at a time. This makes everything so much easier since there is always tension on both the tremolo (or tailpiece) and the bridge from the remain five strings.
9) Rock on!
The technique of comparing the 12th fret harmonic to the fretted 12th fret tone can be applied to any guitar. Just do exactly as is described above for adjusting your string saddles or whatever. Good luck!