This is pretty dependent on the school. Some schools will ask you in the secondary if you'd also like to be considered for MD admissions and will just pass your application to both admission committees at the start of their cycle. Some schools will only pass you to the MD side after they've considered your MD/PhD application and rejected you.
The issue with the second option is this typically happens very late in the cycle. If you're an absolutely stellar applicant for MD you *might* have luck but your chances are extremely slim because the vast majority of interview slots have been extended.
Also, just my .02 but I would really think about what you want your future career to look like. If you don't envision running a lab and having research be at least 50% of your career I don't really think it's worth it to apply to MD/PhD programs. Likewise, if you can't imagine your career without a large chunk of research maybe consider doing a full MD/PhD cycle. I personally think that applying to both programs simultaneously makes you a little less competitive for both. Typically an AMCAS application reads as an "MD/PhD" app or an "MD" app. It can be hard to talk about enough research in your PS to justify the MD/PhD while not focusing on it so much that it will alienate MD programs. But that's just my opinion!
