If you are embedding a Juicebox gallery in an existing HTML page alongside other content, then you do not need to upload the gallery's own 'index.html' file at all. It is required only if you want to display the gallery on a web page of its own or if you want to load the gallery into an iframe.

Alternatively, you could upload the entire gallery folder (not just the contents) to your web server and use the baseUrl method of embedding as documented here.
In doing so, you can keep the gallery as a self-contained entity with all the gallery files stored inside the gallery folder (so there will be no chance of any conflicting filenames).
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) are correct.