That's going to get sticky. Your first MCAT is going to be reported to AMCAS automatically. If you check the box that says you're planning to retake, schools will hold your application until the new scores arrive. Of course, if you get a great score, you won't retake. I'd imagine you could contact each school and let them know you're not retaking and that you'd like them to proceed with their evaluation of your application...
-z