Last year I had to send letters to both places, but I sent the same letters. I think it was pretty much the same as most places. However, there was also a space where you could add an additional couple of letters to be sent only to the MSTP, and I had one of my research supervisors (who hadn't written one of my other letters) write one and send it in.
It's a cool program...I was very impressed by it. I really liked the idea of rotations being optional, and the med school classes being videotaped is also pretty cool.