The point of using a macro rail is to help increase the overall depth of field of the final image. When shooting things close up, only a thin portion of the subject will be in focus as the short distance to the subject causes a very narrow focus area (there are other factors but we don't need to go into too much detail here).You have got some bits right and some bits wrong.
The main point is that you should be trying to keep the same composition as possible; moving sideways is completely wrong. You should be moving front to back not side to side. First compose your image in camera to be pretty much what you want the final image to look like. As you have a rail to help with the depth of field you can also reduce you aperture a bit. This will allow you to get more detail in your final image. Next move the camera/rail so that the very front of the flower is in focus, or even just a little bit in front of that. Take a shot, the turn the knob on the macro rail so that the focus point moves back slightly. You want to try to get a bit of overlap of the focus area between each frame to get a successful stack at the end. Keep repeating this until you have frames captured that move the focus point throughout the full distance of the flower, the final few frames should probably be focused just behind the flower.
If you can't get the whole flower in, then yes you may be able to move the camera sideways and stitch the images together to create a panorama, but that's not really the intended purpose of the rail, and not what stacking is about.
When stacking for depth of field as described above, you move the focal point forward of backwards using the rail. As such you don't want the camera to adjust where the focus is when you move it on the rail; switch any autofocus options off, you want to be in manual mode, and don't adjust the focus between frames.
Hope that makes a bit more sense, but let me know if I've misunderstood what you are doing.
