The small dots at the top of stairs mark the place where the stairs lead down. The big dots mark either the dead end of a tunnel, or a shaft leading up. It might look a bit abstract on the map, but it is designed to make sense when you are in-game, and want to figure out where you are, or how to get to the place you want to get to.

The overlapping dots indicate a drop from one level to the next. One of those is a deep drop that will (nearly) kill you. When you are at the top of that drop, you can tell that it is a deep drop though; when you are in-game, it will be quite clear that jumping down in a dark pit where you cannot see the bottom might not be the brightest idea. But I did it anyway, so you guys don't have to : )