Hrm... don't take me as a definitive reference on this, mate. I considered doing an MD/PhD myself, although for reasons I'll set down in a minute, I decided against that.
First off: how you apply depends on the college. For instance, at UNC Chapel Hill, where I considered doing my MD/PhD, you apply for the MD/PhD program itself instead of for the MD AND the PhD. It used to be the dual application route (and still is at a lot of schools, I believe), but now it's just one application.
Second: if you want to do mostly research, an MD/PhD is fine. But if you want do be more clinical than a researcher, forget the dual degree. The reason I say this is that TOO much time goes into getting an MD/PhD to justify going out for a residency on top of that (and you need a residency to do anything as an MD nowadays). That brings me to:
Third: I think... but don't hold me to it... that the programs used to be just lumped together. In other words, you took the same length of time to do both the MD and the PhD, and sheesh! Talk about overkill! Nowadays, just about every MD/PhD program I've looked at (UNC, UFl, U-Miami, U-Cal, etc) divides it up in pretty much the same way. You do your first two years of med school, and then do three to four years of your PhD, and then go BACK to med school for a final one to three years and get your MD. Yeck...
For me, that last part is what really buggered me. I'm planning on specializing in cardiothoracic surgery, and that's a total seven years residency... and I'm not about to add another three years for my PhD! Hope this helps you out: I remember spending months trying to find out about the MD/PhD programs and not being able to.
Best of luck in all your endeavours! Who knows... you may just be that MD/PhD I couldn't be!
Jason