The best investment I ever made in my D&D gear was to order a custom plastic gaming mat at my local Stapples. For something like 25 bucks I have a plastic mat which contain nothing more than a few hundred of squares of the right size from one side of the mat to the other.
Then I bought pencils for dry boards with a dry eraser and I simply draw whatever I need directly on the mat.
To answer your question, when I have several levels of the same location to draw, I use different colors (I have 4: black, blue, green, red) and I use dots instead of full lines to picture the lower levels.
Make drawing a dungeon with several tunnels holding the whole thing together fun and easy!
For flying creatures... Well, I simply get them higher somehow on the mat and I remember where they are exactly. I guess I would do the same if there was some kind of way for going infinitely down too.