Ryan is always very helpful over in Drupal. I'm not sure you need his help on this though. If I understand the requirements, you want to have different audio files for different albums? The audio file that gets used is specified in the xml file that's generated when you create the album using juicebox builder on your PC. A section from one of mine looks like this:
<?xml version="1.0" encoding="UTF-8"?>
-<juiceboxgallery playAudioOnLoad="true" audioUrlOgg="01 Time The Conqueror.ogg" audioUrlMp3="01 Time The Conqueror.mp3" autoPlayOnLoad="true" enableAutoPlay="true" resizeOnImport="false" importTitle="NONE" showImageNumber="false" captionHAlign="CENTER" importCaption="IPTC" captionPosition="BELOW_IMAGE">
-<image sourcePath="D:\jboxgalleries\frank\base\frank-1.jpg" linkTarget="_blank" linkURL="images/frank-1.jpg" thumbURL="thumbs/frank-1.jpg" imageURL="images/frank-1.jpg">
-
For Firefox at least you need a mp3 version and a ogg version. There are free mp3 to ogg converters on line.
I generate the files (jpgs, xml, audio) then ftp them to my Drupal site. Use the embed in Drupal instructions that are listed on this site.
To keep things manageable, I have a /jboxmusic directory on my sites/default/file directory in Drupal Drupal treats this as a public directory and the javascript program is able to find the music files.