Masking is a practice that comes from printmaking. You mask off parts of the print that you don't want colored on that run. On the next run, you pull off that mask and add another color to that area while masking off others.
In photography and iphoneography, you may have elements in two different photos that you'd like to combine into one.
In this case, I had one version of the photo on my iPhone in which I liked the fish and another version in which I liked the background. In the app PhotoForge2 I added two layers. The first photo I loaded was the favorite background. The second photo I loaded was the favorite fish. But PhotoForge2 uses a last-in-first-out method so my top layer is now the last photo loaded! The favorite fish!
The order matters because it dictates which thing you mask out. Since the favorite fish is on top now, I have to mask out the background of the favorite fish in order to let the background come through from my favorite background now in the bottom layer.
Here's an easy way to look at it. Cover up with a mask what you don't want to see in the top layer. This allows what is in that area in the bottom layer to come through!
Masking is a pretty useful and critical skill. If you can master this one on your iPhone or iPad a whole new world of iphoneography possibilities opens up!