You are probably going to have to apply separately to MD programs and PhD programs. Assuming both programs at a single institution accept you, then you'll have to work it out with them how to organize your MD/PhD. Your PhD years will likely be funded somehow -- you can either apply for a grant, or teach some undergraduate classes, or work as a grader, etc. Your MD years will likely not be funded unless you get a merit scholarship from the medical school. Furthermore, unless you can get some cross credits, there will likely be no time compression.
Harvard has a MD/PhD program in health policy, and you can choose to focus on political science for your PhD. I don't think the MD years are funded, though.
CWRU has a MD/PhD program in heatlh services research. Both the MD and PhD years are funded (through a grant from the Agency for Healthcare Research and Quality), and you take PhD coursework during your first two MD years so that there is some compression of time. But, while CWRU has a political science department, it would be highly unlikely that you could get your dissertation to fall within the bounds of the health services research program.
Quite a few years ago, Greg Pappas (who eventually went to work as the Surgeon General right hand advisor) did a MD/PhD in anthropology at CWRU, but his MD years were not funded. And there was no time compression -- he took 4 years for the PhD in between his medical school years.
Cheers
-AT.