The way it works is, you mark the cuts on the face of the tile, and cut to your marks. The inside corners of the cuts will still be attached. Flip the tile over, and extend the cuts on the backside.
You'll notice you can cut a little past where the cuts intersect, without affecting the appearance of the face.
Sometimes, you can't get the cut all the way through at the corners. No problem. Two ways to approach this, and without knowing your material, I can't say which way it will be best. First, as long as the cut is mostly through, and the cutout isn't too close to the edge of the tile, lightly tap the front side of the cutout with a small hammer, until it comes loose. Second, on the front, cut an X across, connecting diagonal corners, and try tapping with hammer. If needed, flip the piece over and extend the X cuts until the piece is loose, or can be tapped out with a hammer.