The only folder you need to upload to use WP-Juicebox is the plugin folder itself ('wp-juicebox') to the '/wp-content/plugins/' directory.
The '/wp-content/uploads/juicebox/' directory is used internally by the plugin to store files created by the plugin itself.
It is not possible to manually upload files to this directory and have the plugin find them and somehow use them.
The plugin creates its own galleries (from within the WordPress interface) and cannot display galleries which have already been created (for example by JuiceboxBuilder-Pro).
For reference, instructions for using WP-Juicebox can be found here.
If you want to embed a gallery which you have created with JuiceboxBuilder-Pro into a WordPress page or post, then you could use the baseUrl method as documented here.
Essentially, once you have created a gallery with JuiceboxBuilder-Pro, you would upload the complete gallery folder (not just the contents) to your web server and paste the baseUrl embedding code into the body of your WordPress post (ensuring that the method of entry is 'Text' rather than 'Visual'). It does not matter where on your web server you upload your gallery folder to as long as the two paths in the embedding code (the path to the 'juicebox.js' file and the baseUrl itself, pointing towards the gallery folder) are correct.
If you choose to use the baseUrl method, then there is no need to use WP-Juicebox and you should deactivate the plugin to avoid loading the 'juicebox.js' file into your web page twice.
I hope this helps to clarify things.