First, you will want to get the bed Calibrated which you can find here;
Then you need to Set Focus as you can read about here;
Doing that should get your image much closer to WYSIWYG. In addition, by putting the whole image in one file lined up correctly with different upper and lower colors and holding the work in a fixed horizontal direction you can use the Arrow keys or Shift Arrow to move the work in a vertical direction only that will help a lot. Making sure to use the focus on the same place so the perspective is the same. I often do this several times to make sure .
As a last resort do a test run that can abort at top speed and power of one to double check that alignment. It might even be a good idea to make a small mark off to the sides to run that test.