1. How do you properly intonate it because of its fixed position and "saddles"?

2. How low should the stopbar be- and this goes towards TOM bridges too because I have a Les Paul and I want to know how low the stopbar should be.
Which wrap around bridge are you talking about? Most that I've seen have adjustable saddles for intonation.

as for the TOM stop bar - in a lot of cases you can have it all the way down as far as it will go and that's fine. You only need to raise it if the angle is too steep and you're getting string breakage, OR you want a looser feel on your strings. I have two guitars with a TOM bridge - one I have the stop piece all the way down, the other is raised a bit. It's really just what works best for you and the particular guitar.
Note :
Wraparounds on PRS's are compnensated, IE they'll be pretty much intonated at standard tuning with 9s/10s
and they do replacement bridges for higher gauges.
Quote by konigstiger
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Damn right I am.

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Alright that's good then. I play with 11-49's and I wanted to make sure that it wouldn't mess up the intonation on a wraparound.