First of all, you need a program that can save a png file, like Paint.NET. You need to change the opacity of the layer you want transparent from 0-255. 255 is a completely opaque layer, 0 is completely invisible.
If you are on Paint.NET, find the layers window. Click the icon with a tag and a pencil, that should be properties.
You should see this window. Drag the "Opacity" slider to a transparency of your choosing.