Here's what I did, after reading a bit about it: Take the measurements, just as westhemann described, to find your scale length. Now, I assume your bridge has adjustable saddles? If so, then adjust the saddles so that they are about 3/4 of the way extended--if the bridge was on the guitar, that would mean that they were adjusted 3/4 of their range of travel toward the neck.
Now, just as westhemann wrote, the length of the strings from the edge of the nut to the point where the strings cross the saddles needs to be as close as possible to the scale length of the guitar. Most Fender-strat or tele type guitars use a scale length of 25 1/2 inches; a lot of Les Pauls use 24 3/4 inches; Paul Reid Smith uses 25 inches even; but do the measurement thing to be sure! Position your bridge as accurately as possible so that the point where the strings will cross the saddle is exactly 25 1/2 inches (or whatever your measurement comes up with) from the point where the strings leave the nut. (You also want to be sure, sure, sure that the bridge is centered so that the strings won't be off to one side on the neck.) Mark the spots to drill your mounting holes with the bridge exactly where you want it!
Now the good news: adjustable saddles give you a bit less than a half-inch of leeway to adjust the individual saddles to get just the right string length after the bridge is installed, so perfection in mounting is not required. I'm a complete amateur, and the bridge position was just about the only thing I got right the first time I did it on my first guitar.
Of course, after you get the instrument strung up you'll need to adjust the saddles some in order to get it to play in tune--because each string is stretched slightly when you fret it, a string that is exactly 25 inches long on a neck made for a 25-inch scale length will sound ever so slightly sharp when it's fretted. You compensate for that by screwing the saddle back toward the bridge end of the guitar, making the vibrating length of the string very slightly longer. And because each string is a different gauge, each one stretches slightly differently and you have to adjust each string individually. Take a look at a well-set-up guitar and you'll see that the individual saddles are staggered. If you do it by ear, you're trying to get the harmonic tone produced by touching the string lightly exactly halfway between the nut and the saddle to precisely match the sound of the same string fretted at the 12th fret.
I apologize if you understand all this already. I tend to blab on and on.