We've just been certified to both standards as of this week.

One of the things I had to do was to create separate scope statements for the two standards. Our customer base is divided up between Industrial/Automotive, and Medical. I broke my scope statements out between the two sectors, with Industrial/Automotive meeting 9001, and medical meeting 13485. So we still have ONE integrated QMS that meets both standards. We continually improve the QMS elements related to our industrial customers, and we maintain the effectiveness of the QMS elements related to our medical customers.
All of our reporting, e.g., mgmt. review, goals and objectives, KPI's, etc., are broken out by sector and reported separately. We perform risk mgmt. for our medical customers, but not for our automotive and industrial customers.
I struggled mightily putting it all together, and getting us to this point, but having now gone through the process, it's turned out to be much easier than I thought it would, and if I had to do it again, I'm pretty sure it would be much easier.
I hope this helps a little...