I'll try to explain how to basically get your guitar in tune, with the bridge parallel with the body.
You say your bridge becomes higher when getting your guitar in tune, did you put a higher gauge of strings on it?
If you put a higher gauge of strings on, you should adjust (tighten) the springs in the back of the guitar, who are attached to the trem.
Best thing to do when the bridge is too high is tune the guitar below the wanted tuning, and just tighten the springs. As they get tighter, the bridge becomes lower, and the pitch of the strings gets higher.
Do this a couple of times till the trem is parallel to the surface of the body, and till the strings are in tune in that position of the trem.
However, if you cant tighten the springs anymore, and the trem is still too high, go out and buy an extra spring.
If you put on a lower gauge, just do the exact opposite of all of this.
Usually when changing strings, especially on guitar with floyd rose trem, its a good thing to adjust the trus rod of the neck, and the intonation. If you dont know how to do that properly, you could mess it up though, so its best to let a tech set your guitar up properly (not everytime you change strings, just when you change gauge).
I hope this helps a bit, and if someone sees something i said is absolutely wrong, please tell me! hehe
Greetz TK