fret the low E on the 2nd fret and 12 fret and look in the middle(around the7thfret),
This creates a straight(the string)by which to judge,It doesn't have to be straight to be right,some people prefer a bit of relief on the neck.
I always thought it was the first and the last fret (22 or 24), then look at the 12th fret. There should be a small gap, depending on your action height and or preferences!
Fret the E string at the first and last fret. The distance from the string to the fret on the 8th fret should be about .010" , but in reality is up to the players preference. I set up mine on the high, or small E string, just because it's easier for me to see the gap there. In the end, it really doesn't matter what string you use, because you are basically just using the string as a straight-edge. Anyway, I use a standard piece of paper as my gap measurement on the 8th fret on the high E string.
Remember, only turn your truss rod about a quarter-turn at a time until you get it where you want it.
Two good references for setting up your guitar are:
The Wolfgang Owners Manual from Peavey. This one is particularly helpful with EBMM guitars since the truss rod adjustment is the same as all EBMM guitars.
The PRS setup guide as found at the PRS official website. You can get a lot of good measurements there. They give you the factory tolerences for a PRS guitar, which you can use as a baseline for adjusting your guitar how it's comfortable for you.