Hi,
There's a way to do it, but it's quite complicated.
I've never used the software you use, so I don't know exactly how it works. Most image editing software allows to to create a transparent layer. If you create one and then remove the other background and save, instant transparency! The only problem is, Internet Explorer and other browsers that use it don't show it as transparent. To get it transparent you'll need to download ImageMagick and execute a small script on each file. It's a little complicated, but I can give you the script if you want it. 
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