Questions about creating a wordpress logo

I have an HTML5 site picked out at 3DCart and I am getting ready to make a badge prototype logo and am want to know what I am doing to remove the backing after i crop the images, I have duplicates of same object except one will have a cutout image and the other still has checkered backing? I am using the Vintage Badges to collaberate my ideas for when i have someone create a logo for me this is a prototype website and logo