Depends on the program. Most that I know of allow you to apply anytime to the business school during your first 3 years (that is assuming the 5 yr program is structured so that you do the business school aspect only after completing the first 3 years of med school).
I'm only, and just barely, an MIII, so take what I say with a huge grain of salt, but coming from someone such as myself who has been interested in the dual degree for a few years now and has done lots of research on the issue...I would say that an MBA would NOT directly help you run your own practice. [btw, there are lots of threads on this topic. I'm just sharing this with you because I feel like it's my turn to say what has been said before]. There are several reasons for this: 1)By the time you finish med school and residency AND are ready to open up your own practice, who knows what you remember from your business education. 2)A general MBA will give you a general knowledge about accouting/finance/management/marketing but you'd have to know quite a bit about managing a practice already to really get anything out of it. Which brings me to my next point. 3) I would recommend waiting on the MBA until after you have practiced for a bit (yes I know but if you do it now you'll be saving time and $$...well that's fine but you really wont gain from it as much as you could with experience in the real world already under your belt). 4) I think an MMM would prepare you more for learning how to manage a practice. 5) If you did wait until you were a licensed physician, you could enter an executive MBA program that would much more cater to your specific career goals.
There are many more reasons for and against the dual degree but if by the slightest chance what I have said is new to you, then I hope I've helped in some way.