I'm going to try and build a fort based around siege difficulty- the main entrance is heavily guarded and trapped, the secondary entrance really isn't an entrance but a way to release land forces to the enemy, a link between agriculture sector and main sector that is heavily secure (A minecart bridge/walkway that's only open when the drawbridge is down for the main sector and when the main fort has "accepted" travel via another lever). The agriculture sector is likely the least secure, as trading will also happen here, as well as animal pastures and possibly cavern breaching. There's a third way in connected to this, but you have to go from the surface down to the caverns and up again, so it won't be easy.
There's a third building connected to the main sector via underground that also breaches into the caverns. This one is as secure as I can make it.
The mainsector entrance has a moat, archer barracks, and a cave-in ring. The agriculture subsector has only a bridge and wall.
The third building has only a door (as it's going to connect to the caverns, and not the rest of the fort directly through anything but a bridge.
---
A secondary plan is to subsector the fort in three ways: the main sector which handles mining and production of goods, the agriculture subsector which is almost entirely aboveground including a minecart bridge and walkway, and the Expidition subsector that indirectly connects to the fort and the caverns.