Please see the section entitled Embedding Multiple Galleries in the 'Juicebox - Embedding Guide'.

You could build a multiple-gallery website manually using the examples in the link above as a template.
You could also use the Juicebox Skin for jAlbum to create a multiple-gallery album in a single pass.
Once you have installed both jAlbum and the Juicebox Skin, you would be able to drag and drop an entire folder structure into jAlbum's main window. After clicking the 'Make album' button, jAlbum would create a Juicebox gallery for every folder/subfolder in your input structure and all the galleries would be linked together and accessible through a JavaScript navigation tree. Here is a sample album (comprising one folder with one subfolder) created with jAlbum and the Juicebox Skin.