Do not hesitate to call programs and ask if it is too late to send in your application. At some programs you may have all ready missed the deadline. At others you still have time if you are quick about sending in those extra secondary essays.
If you are too far gone in the application process to change to MD/PhD you can still try and get into one of these program once you start medical school. Speak to the MD/PhD program director at your medical school about how to transition. Usually this means you pay for the first two years of medical school, demonstrate interest in research over the summer and they decide whether or not to admit you before you need to sign up for third year rotations.