We have a video on YouTube entitled How to Build a Web Image Gallery in 5 Minutes which you might find useful.
Also, instructions for embedding a Juicebox gallery in a web page can be found in the Embedding Guide.
If you want to embed multiple galleries throughout your site, then I would recommend using the baseUrl method of embedding documented here.
Essentially, once you have created a gallery with JuiceboxBuilder, you would upload the entire gallery folder (not just the contents) to your web server and paste the baseUrl embedding code into your web page where you want the gallery to appear.
You can upload the gallery folder to anywhere on your web server as long as the two paths in the embedding code (the path to the 'juicebox.js' file and the baseUrl itself, pointing towards the galley folder) are correct.
Keeping each gallery as a self-contained entity (each gallery in its own folder) should help to keep things organized on your server.
Also, you can have all galleries throughout your site share a single 'jbcore' folder (rather than have each gallery use its own 'jbcore' folder). Please see here for details.
This has the added advantage of being able to upgrade all galleries at once (when a new version of Juicebox is released) by replacing just one 'jbcore' folder on your site.
If you use the baseUrl method of embedding and have all your galleries share a single 'jbcore' folder, then you could paste the baseUrl embedding code into your template.
As long as the path to the 'juicebox.js' file is correct in the embedding code, the only thing that would need to be changed for each gallery is the baseUrl itself (the path to each gallery folder).
If you are looking for an automated solution to creating and listing multiple galleries, then you might be interested in another one of our products - Showkase.
Showkase is a PHP web application which allows you to create a complete portfolio web site (integrating multiple galleries) online.
Showkase has full support for Juicebox-Pro (and SimpleViewer-Pro) galleries and the galleries can be created within the application itself in a web browser interface (or created with JuiceboxBuilder and imported).
You can create Gallery Index pages and have as many galleries listed on each Gallery Index page as you wish.
Each gallery is represented by a thumbnail image with the gallery title displayed below and the gallery is opened when the user clicks on the image.
Demo sites created with Showkase can be found here and a sample Gallery Index page can be found here.
Showkase can also create non-gallery pages (About, Basic and Contact pages) where you can add information about yourself (or any other content you like).
All of this is done automatically within the Showkase interface without the need for any manual coding at all.
Showkase can be purchased as Showkase-Standard (which comes with Juicebox-Lite and SimpleViewer-Standard, the free versions) or Showkase-Pro (which comes with Juicebox-Pro and SimpleViewer-Pro).
The only difference between Showkase-Standard and Showkase-Pro is the bundled viewers.
More information on the differences between Juicebox and Showkase can be found in this forum post.
I hope you find this information useful.