So I started with the main entrance. Right off the bat I got the multiple level effect across by using a stone bridge over the entrance passage. To accent that the raised sections weren't the primary part of the fortress, I've made the stairs in that section a mix of man-made and natural formations.
You can see how my map drawing technique works in this partially done piece. I draw out the sections, and then go back and double-up the main walls, then add the cross-hatching. One of the big advantages of the cross-hatching is also shown on this map - the obvious one is that it makes the stone walls dark and "stoney", but it also makes it so when I white out the grid lines, I can do it quickly without damage to any of the walls, and the grid lines are barely visible in the cross-hatched sections.
This in-progress shot was scanned and a slight increase in both brightness and contrast was applied. For a final, I would increase contrast significantly more to make my pencil drawings look more 'inked'.