If you are using the embedding code generated by JuiceboxBuilder-Pro (and presented on the application's 'Publish' tab), then you should follow the regular embedding instructions here and upload the contents of the gallery folder (not the gallery folder itself) to the directory that contains the HTML web page into which you have inserted the gallery's embedding code.
If you have uploaded a complete gallery folder to your web server, then you should use the baseUrl method of embedding documented here. The baseUrl method of embedding uses similar embedding code to the regular method but with a baseUrl entry pointing towards the gallery folder (so that Juicebox knows where to find the gallery).
For example, if you have a gallery folder named 'my_gallery_folder' and you upload the complete gallery folder to your 'ht_docs' directory, then you can use the following embedding code (changing the gallery dimensions and background color as necessary):
<!--START JUICEBOX EMBED-->
<script src="/my_gallery_folder/jbcore/juicebox.js"></script>
<script>
new juicebox({
baseUrl: '/my_gallery_folder/',
containerId: 'juicebox-container',
galleryWidth: '800',
galleryHeight: '600',
backgroundColor: '#222222'
});
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->
The leading slashes in the paths above denote your root directory (in your case, your 'ht_docs' directory) so the embedding code above will work in any web page throughout your website without modification.
I hope this helps.
However, if you continue to experience difficulties, then please let me know and I'll try to help further.