MSUCHM (the MD college) and MSUCOM (the DO college) never took classes in year two together. In year one, some of the basic medical sciences are taken together (not all, one example is gross anatomy). However, for the incoming classes this year the two colleges will be completely seperate and will not be taking anymore classes with each other at all.
Michigan State organizes its medical programs (and other programs) as "colleges" and not "schools". One implication is that some of the facilities are shared, along with professors, who can also be shared with other departments of the university other than the medical colleges. So in the first year basic medical sciences, these courses were taught together (will not be for the incoming classes), so yes some classes were taught from the same building because both MD and DO students took the classes together (albeit different standards: MD pass rate 75% minimum, and DO pass rate 70% minimum usually, and this varies from class to class). The MD school has 2 preclinical campuses, one in East Lansing and one in Grand Rapids. So the Grand Rapids campus has completely separate facilities altogether. At the East Lansing campus, although classes will be taken separately for this incoming class, students will still share the anatomy lab with the DO students (and even other types of students). However, the "home bases" will always be separate, Radiology and the Life Sciences building for the MD students, and Fee Hall for the DO students. And I suppose all of this will only make sense if I mention that the classes were taught at certain locations and then broadcasted live (and recorded for later use) to the other locations (ex. the DO campuses at Macomb, DMC and the other MD campus at Grand Rapids). Usually, most of the lectures came from the East Lansing campus and broadcasted to the other satellite MD and DO campuses. But supposedly, especially since the classes will be taught completely separate from each other, where lectures are physically given will even out between campuses (professors will rotate).
I hope this clears some of the confusion.