Well the basic topic of this thread is pretty obvious. Since dwarves rely on various crops from the caverns, they must have a way to get them. Therefore, the mountain homes should have some access to the caverns. This could take the form of a nearby cave entrance, a deliberately constructed tunnel down to the caverns, or a passage directly from the mountain home to the caverns (heavily fortified, of course).
However, there are related topics, such as the fact that in all likelihood dwarves originated in the caverns. I'd say that the earliest mountain homes would have started from the caverns and only afterwards would they have been connected to the surface. Some might only be connected to the surface by a distant tunnel entrance in fact! Dwarven villages probably exist in the caverns, but only with defenses against the dangers of the caverns. I touched upon this topic in my "I want to embark in the caverns" thread. However, I thought that it would be good to bring up the subject directly and in more depth now that Toady is working on cities and the like.
I believe that the dwarves would have originated in the caverns. They're use of subterranean plants and affinity for earth and metal is evidence of this. However, since the caverns are so dangerous once the dwarves discovered the surface, they would have colonized it. However, it is likely that many dwarves still live in settlements in or carved off of the caverns, due to limitations on how much surface land they could claim (after all, the surface races would have already been established and would claim much of the surface) and the fact that no matter how dangerous the caverns are they are ideal for dwarven life. No doubt wars would be raged for control of surface regions desirable to the dwarves. It's also likely that dwarven armies patrol parts of the caverns that are claimed by dwarves, driving out the more dangerous denizens the best they can. It's likely that fortifications, similar to the human castles that exist on the surface, would exist in the caverns.