Probably the best place for you to start is to learn to make sure the wheel is seated in the dropouts exactly the same way every time. Otherwise, any disc brake alignment is going to be off most of the time.
The trick is to have the weight of the bike on the wheels and loosen the QR. When the QR is open rock the frame and the wheel a little until you feel the axle settle in the dropouts. Once it feels seated correctly then slowly close the QR. Watch the axle/dropouts and make sure they don't move around as you tighten. Finish closing the QR and that's it. Assuming your frame, or fork, is not bent, you should be able to view the wheel head (or tail, for the rear) on and see that the gap between the sides of the tire are equidistant from the seat stays (or fork legs). That's just a sanity check, but it's a good habit to get into. If your frame, or fork, is a little bent, then you should just shoot for consistancy. But, if that's the case, then you should have the wheel's dish checked for sure. I've seen a LOT of wheels that show up not centering properly and then turn out to have bad dishes. But, I digress. That's another issue.
If you are careful about this, your rotors will line up properly with the calipers most of the time. Practice, practice, practice ;-))) You will get better quickly.
Obviously, the caliper alignment must be done with the wheel properly seated, to start with.
Also, it's not unusual for brand spanking new rotors to be out of true. Get this checked at your LBS.
Last edited by cascade168; 09-28-08 at 12:34 AM.