Hello my friend.
The intonation its easy to change on the PRS SE models with a stoptail bridge.
You'll need a little L (a small allen wrench provided with your new guitar) shapped tool to change it. You have to use that tool in two little holes.
I uploaded a picture pointing to the spot of the holes where you can adjust.
I strongly recomend you to change the intonation, since the PRS models comes from factory with a bad tuning at 12th fret.
If you tune your strings with a tuner, and check if the tuning at 12th fret its ok, you will see that it has a little diference.
Don't forget to first detune the instrument before you start adjusting, to relieve the tension on the bridge.
First you must start with the treble side and then pass to the bass side, and the return to the treble side for one last check.
If you need anything, I can help you in.
JB