As someone in the trenches of the JD/MBA application I can comment:
For most schools you need to apply separately to each and its highly possible (and I'm highly dreading) that one could get into one program and not the other.
There are a couple of notable exceptions to this. Northwestern's JD/MBA admissions is done via a single application through Kellogg. You need only submit your GMAT score (this is unique). I think this is because Kellogg is a bit more difficult to get into than Northwestern Law is.
NYU has a combined form as well, but you only submit your LSAT score. I think this is because NYU Law is somewhat more difficult to get into than Stern.
For every other school that I have looked at (ie all of the top 15 law/business schools) one must apply to both schools separately. If you're going JD/MBA...have fun and good luck!