Good question. I've not yet tried it in the new SW, but you might be able to do a work-around. If you tell the decal (in the properties when you set up your decal) to follow the settings of the SW material, you might be able to adjust your material to be somewhat transparent.
Here's another way I can interpret your question: When you create your decal, use a solid particular color for your background. When you apply the decal, on the second tab (image or something like that), select the background color to be transparent, or masked out. The interface is a tad awkward, but it works. You can either select the color with a pointer or select the absolute color in the color palate. When the decal renders, the selected color will not be seen. I believe you can select multiple colors, but this can be cumbersome. I recommend using something inexpensive, but effective such as PhotoShop Elements (need layers) for editing your decals for rendering.
One of these days I'm hoping to post a tutorial on a simple scene for this stuff since it comes up so often. (Where can I buy about five hours to get this done?)
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