... was confused by some of the terms such as JuiceBoxBuilder
Just to clarify, JuiceboxBuilder is the desktop application which comes with Juicebox to allow you to create and edit galleries on your computer. More information about JuiceboxBuilder can be found here.
As long as you know the location of the images, then you can build the gallery manually following the instructions here. Step #4 is where you would enter each image URL and caption.
Rather than start from scratch with the sample 'web' folder, you could create a gallery using JuiceboxBuilder-Pro (with a couple of sample images) to customize the gallery as you like (using the configuration options on the 'Customize' tab) and then just edit the 'config.xml' file afterwards to change the <image> data.
If you know that all the images for a gallery are going to be in a certain folder, then you could use a server-side scripting language (such as PHP) to dynamically create the required XML file. An example of how this could be achieved can be found in this forum thread.
I do not know how you will be receiving the data but if it is always in the same format, then you could perhaps write a PHP script to convert what you are given into the correct format for a Juicbeox gallery's XML file.
I hope this points you in the right direction.