Like others have posted, you have to basically cut your molding upside down. On your mitre saw, you have to position the portion of the crown molding that will be against the ceiling on the base of your mitre saw, and the portion of the crown molding that will be against the wall on the fence of your mitre saw. Keep in mind that if you need to mitre the left of the molding, the mitre will be on your right on your saw. Then you flip the molding over and it should line up, providing your corner is exactly 90 degrees. Also, make sure you hold the piece of molding at exactly the same angle on your saw as it will lay on your wall. For this, cut a small piece of molding about 1 foot long, and lay it against the corner of the ceiling and wall the way it should go, and make a mark on the ceiling and another one on the wall where the crown molding ends. Remove the molding, and measure the distance, on the ceiling, between the corner and your mark. Transpose that mark on the base of your mitre saw.

For beginners, it can help to put a piece of painters tape on your fence and write "wall" and another piece on the table and write "ceiling".