The inside is usually made of one or more "living" levels, with a large central plaza (suspended above a shaft, sometimes) with bedrooms, the common dining room, the hospital and a lever room. Sometimes I made a common people level and a noble level.
Then there's the worksops and storage level (no fixed layout for those, it depends on the terrain), and under all of that there's the mining levels, whose entrance is usually separated from the main base, so that I have time to seal it with only minor losses if something goes wrong.
The military area is behind the gates, and I always try to make the gates themselves somewhat like al Khazneh in Petra (
http://www.industriadelturismo.com/wp-content/uploads/2010/11/Petra-01.jpg).