My first real attempt to live in the caverns went from fun to annoying to downright brutal. I quickly built some walls and doors; or rather, quickly ordered them to be built. A giant rat managed to run all the way up the stairs and drink some booze before I could toss the new recruits at it. Giant rat steak was just coming off the grill when a giant toad stopped by. At this point I realized my doors weren't working and started replacing things with walls. This was after the doctor had his head bitten off. Now, comfortable but shaken, life returned to normal. Then a giant bat thwarted my two-dimensional defenses. After the massacre(s), I abandoned.
I'm thinking I'll go for a natural progression from above-ground to the top layers of rock, and then to the caverns. There's enough ore and gems in the solid rock to get a fort really going, assuming we don't starve to death. Once the army corp of engineers is sufficiently armored and trained, we'll begin systematically exploring, expanding, and partitioning the caverns for living and working spaces. The "old" fortress will be maintained for whatever topdweller purposes we might have, but the real industry will go where dwarves belong. Each successive cavern layer will be explored appropriately and converted for civilized life.