depending on what program you use, when you hit save as, there's an option to make it Transparent. For example, in SAI, when you save something a little box should pop up and you want to choose the second option I believe - its something like "all pixels have opacity" or something or in Photoshop, you just simply delete the background layer. If you use MS Paint, the only way I know how to save it "transparent" is to just fillbucket the background the green dA colour.
There's your problem. You aren't working in layers to begin with. If you prefer drawing in Paint, then when you upload the drawing into PS, take the magic wand tool and select outside the drawing. Then press delete.
This is absolutely fantastic! Seems like every deviation you have some new improvement or technique to show us, which I think is absolutely fantastic. It's always inspiring to watch art/artists in motion.