The Atlas is book that contains the outlines of the various Regions. Currently the game has two atlases. The first atlas you start with and can be seen when you press "m" by default. This brings up a map which is the users free atlas. It'll show you the region you are currently in. If you zoom out, it'll be blank. This map gets assigned way points as you discover places. The second atlas, you purchase at a scribe shop and it is blessed. This atlas is accessed via opening the book from your inventory. Its completely blank and will allow you to set your own way points.
There are maps that are available throughout the game that will paint in the outlined regions of the atlas. If you visit any general store, it'll have the map for the region you are currently in. It can be purchased for two silver. You can use these maps in two ways. The first is to open them and memorize them. When you memorize the map, it adds the map to your free atlas that is accessed via pressing "m". Once this is done, when you zoom out, you'll see the region added. You may then click that region and view it despite being in a different area. The second way to use these maps are to right click your purchased atlas, choose "add map", and then click the map. This will add that region to the atlas.
There are two types of way points because there are two types of atlases. There are system created way points that are added to the free atlas and there are player created way points that can be added to the purchased atlas.
There is an interactive Atlas available on this wiki listed as Celador.