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Though the specifics don't match your cartography workflow, Brandon Kowallis's Adobe Illustrator Tutorials (previously on CaveChat) discusses concepts that may help you represent walls and pillars clearly in complex situations.

Pencil color into the rest of the passage, then the pillars will show white, like the rest of the background. That way, since you are drawing by hand, you dont have to worry about a wierd, inconsistently shaded fuzz on the outside of the walls, that Illustrator takes care of with the shading tool.