I know what I need to do, I'm just not sure how to do it.

I got a texture pack for simple textures, no shading or anything, very conservative with the colors. I decided to reskin the mobs too with my own designs but after saving, everything that should be transparent space is black. I'm using MS Paint to edit which opens the skins with black in the transparent areas, then saves them as black. Is there a way to make those spaces transparent after the edit or is it just the program I'm using?

I've attached the texture.

Files: 

3terrain.png