The pen tool is pretty simple. Select it and then each click will drop a new anchor point on your document. Clicking again on the first anchor point you dropped will close the chape. Then, you can edit the stroke and fill. You can select the "open selector" (I don't know if that's actually what it's called), which is the white pointer arrow low down on your toolbar, which will select your shape again if you're chosen another tool or layer.
Pattern overlays aren't too complicated either. You can double click the layer and use a layer style. Click pattern overlay, then choose the pattern that you want to use and it will fill everything in the layer with that pattern. This is non-destructive, and also allows you to adjust the opacity and the size of the pattern as it is displayed. You can also Control+click the layer icon, then use the edit menu and select edit fill and choose your pattern. This however will "erase" the color that your shapes on that layer currently are. Note, that if you draw with the pen tool your Photoshop might be drawing vectors as opposed to just adding pixels, which I like because I was brought up in Illustrator first. If that's the case, in order to edit them you will need to rasterize a layer, which can be done by right clicking on it in the layer menu.
Elevation you can do in a number of ways. You recently looked at my map Cinzienne, where elevation was simply painted on using low opacity brushes on black (shadowed side) and white (sunned side). It's easy to start but tough to make look really good, in my opinion (I don't think I succeeded on my map yet). You can also do it in a more automated way, making it look "faux-satellite," and I suggest taking a look at Ascension's Atlas tutorial if you'd like to try something like that.
As for the other stuff, I don't know much about magical pollution
Hope some of that helps. Happy mapping!