OK, so I just got new strings, trying out a heavy gauge (12-56) and of course after I finish restringing it I realize im not so fond of heavy gauge :| Now that aside, I just have a couple questions about the bridge and dealing with this heavy gauge.

First off, I have a problem with the bridge raising up due to the large tension that comes witha higher tension string. I messed around with the action too, and that helped a bit but the bridge is still raised a bit. Now mu guitar (Squier strat) came with an extra spring that goes in the back to hold the tension of the strings (3 are in there already) Would I be able to rearrange those springs that are there to add the fourth on there to balance the tension, without damaging the guitar?

Another question, probably easier to answer. For a lot of pics of guitars I've seen, the saddles are usually at a slope (of course now I can't find a picture). Why have a bridge with varying string lengths? What advantage does that give over just having it all in a line?
Adding that extra spring will pull your bridge closer to flat against the body, but I would suggest loosening the strings a bit before you put the spring on, as the sudden extra tension may cause them to be pulled sharp and possibly snap. You can tune back to pitch after you put the spring in. This shouldn't damage the guitar in any way, though using the whammy bar could be a bit difficult.

The guitar is an imperfectly designed instrument, so the strings need to be at different lengths in order to have good intonation - ie so that the strings are in pitch on every fret. The frets are a calculated distance apart to produce pitches a semitone apart, but the strings are higher than the fretboard and thus longer than the fret scale, so this needs to be compensated for.
I understand I'll have to loosen the strings, in order to get the fourth spring in I have to rearrange the other three, and I'd prefer the bridge to not rip off towards the neck due to the string's tension. And I figured the whammy would be harder, but seeing as I lost mine due to lack of use I don't think it's too much of a problem.

I suppose the intonation makes sense, but wouldn't it have to be changed based on the gauge of the string, and based on the action? And how can one calibrate the intonation to be accurate?

That was quite helpful, I'm just curious as to how a guitarist perfects his instrument. Thanks
If you really want to get into setting up guitars, you could get this book, which explains everything about how to set up a variety of guitars.
Yuo shouldn't need the extra spring - just tighten the long screw running from the far end of the spring block into the guitar body, this should tighten the springs. Keep retuning to pitch each time you adjust, and eventually the trem should settle level against the body.