The way I understand it is this.
If you add another school and resubmit your application, then the medical schools will receive an electronically downloaded form that indicates a change in your application. If all you are doing is adding a school, then the only thing that should happen is that you get charged some more on the credit card and the additional school will be entered into the electronic queue to the list of schools you are applying to.
Now, if you change it after AMCAS has already downloaded the application to the med school list, then every med school will receive an electronic packet indicating a change of information, and the new med school will just get the original electronic application packet.
Supposedly it should not affect your application as a whole, but who knows really. With all the bugs in this application, I wouldnt chance it unless you are pretty sure that this new school is one of your top choices.
Keep in mind that I base this solely on the FAQ for the medical schools to AMCAS, so take it worth a grain of salt. That FAQ is really long, but if you browse long enough it does mention what happens if an applicant changes the application and does a re-submittal.
Good luck