I would recommend using the baseUrl method of embedding as documented here.
This allows you to upload your complete gallery folder (not just the contents) to your web server. Keeping all the gallery files together inside the gallery folder should help to keep things organized.
It does not matter where on your web server you upload your gallery folder to as long as the two paths in the baseUrl embedding code (the path to the 'juicebox.js' file and the baseUrl itself, pointing towards the gallery folder) are correct.

For example, if your gallery folder is named 'my_gallery_folder' and you upload the complete gallery folder to your web space's root directory, then you could use the following embedding code in any web page within your site to display your gallery (changing the dimensions and background color as required).

<!--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.

Please also see the note regarding 'Embedding Using Dreamweaver' here.