Alpha layer is a layer of nothing, it will be like glass, you can't see it.
Like a gif image.
But!!!
When you save image with it you have to be sure it's no color what so ever where you want the nothing to be.
You can't open a DDS image and save it again with alpha layers, you always have to do a new one.
Open a photoshop image that's transparant and paste the part you like to be seen in it and save with alpha layer.
Everytime you open a DDS image, photoshop will assign a color to alpha layer.
Photoshops on format is only one you can save and open again with transparent colors.
Se other thread for more info...
It feels a little off with graphic school in a SSM forum.