If you are trying to embed multiple galleries into a web site, I would recommend using the baseUrl method of embedding as documented here.
This would allow you to upload complete gallery folders (not just the contents) to anywhere on your web server (as long as you know where they are) without the need to rename or move any files within the gallery folders.
For example, if you had two complete gallery folders named 'gallery1' and 'gallery2' and you uploaded them to the root of your web space (in this example, a domain named 'www.example.com'), then the embedding code for the two galleries would be:
<script src="http://www.example.com/gallery1/jbcore/juicebox.js"></script>
<script>
new juicebox({
baseUrl : 'http://www.example.com/gallery1/',
containerId : 'juicebox-container1',
galleryWidth : '800',
galleryHeight : '600',
backgroundColor: '#222222'
});
</script>
<div id="juicebox-container1"></div>
<script>
new juicebox({
baseUrl : 'http://www.example.com/gallery2/',
containerId : 'juicebox-container2',
galleryWidth : '800',
galleryHeight : '600',
backgroundColor: '#222222'
});
</script>
<div id="juicebox-container2"></div>(When embedding galleries as above, you can still have all your galleries share a single 'jbcore' folder.)
