I was an "in house" candidate, ie I entered the MSTP officially in the winter quarter of my second year. I was initially dissuaded from applying for the MSTP straight out by my undergrad research mentor who told me if i wasn't "absolutely, 100% convinced that the only thing I ever wanted to do with my life was research," i should just do a straight MD. In the summer between my 1st and second year med school, I did a summer research project which worked out really well. I made inquiries, and found out that the program at my school typically (at that time at least--it was a long time ago) kept a spot or two open for in house candidates. It was a sweet backdoor--I only had to compete with other in house candidates, not all of the MSTP candidates.
And now, 8 years later, i'm about to graduate. It's worked out great! Highly recommended if you like research.
The thing to do is get friendly with the MSTP director and the program coordinator.
-mrp