In your mind, just think of layers as several sheets of transparencies/cellophane OHP paper stacked on top of each other. If you draw particular things on separate sheets, it makes it easier to edit because and you can change things on that sheet without affecting the others, or even just remove that sheet and put a new blank one in if you don't like it.

I was considering a cave (with mine) type map similar to this, so I look forward to seeing the end result!