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'.
This is pure gold advice. Thank you very much for explaining your thought process and the reasons behind decisions taken in your work.

Ravs