You can set your gallery's background to be transparent by setting the Background Color Opacity (in JuiceboxBuilder-Pro's 'Customize -> Lite' section) to '0' (zero).

When setting the Background Color in JuiceboxBuilder-Pro, the application sets the backgroundColor configuration option in the gallery's embedding code (presented on the 'Publish' tab and in the gallery's 'index.html' file) instead of in the gallery's 'config.xml' file.

You can easily add a backgroundColor entry to your own gallery's embedding code.
Use backgroundColor: "rgba(0,0,0,0)" to make your gallery's background transparent. (It's the 4th '0' (the alpha channel in the rgba notation) that actually makes the background transparent.)
(Be sure to separate all options within the embedding code with commas.)

For example:

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
    new juicebox({
        containerId: "juicebox-container",
        galleryWidth: "100%",
        galleryHeight: "100%",
        backgroundColor: "rgba(0,0,0,0)"
    });
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

I hope this helps.