I wouldn't worry too much about the secondary yet. I don't think I received mine until October last year (I sent in the primary application at the end of June) and that was without the current AMCAS nightmare. Everything in the admissions office is moving fairly slowly right now.
The MSTP application will be included with the secondary. If they haven't changed from last year, it is a sheet of paper asking you to list your publications and presentations, and to describe your research experience.
Sorry I've been kind of AWOL from SDN lately. As BeckyG noted, we just started classes and are being inundated with material. She of course told me about your question, so I thought I'd respond. If you have any others or need a place to stay when you come for interviews, I'd be happy to help. 😀