When its configured correctly you should not be straining your eyes at all. The stereo 3d works nicely on this title but not by default. You can press F7 and it will save the settings.
You should see an on-screen HUD that says "Depth Amount" with a green bar, similar to the volume display on a tv. I usually have this at 3 or 4 bars. Sometimes you have the hold F5 down, it depends on the game usually Control-F6 is the ticket.