Is the problem that when you tune up (higher in frequency) on one string, the other string goes flat? If so, its most likely because your trem system. What you have to do is just get the strings close to being in tune, and almost anticipate that tightening one is going to cause the others to go flat. So get it close, and then just make smaller and smaller adjustments on each string until you're in tune.

If you are way out of tune, and tune one string at a time, with a trem system like that, the other strings are not going to stay in tune. You can't slacken or tighten one string significantly without affecting the others.