Yes. There are several ways that this can be achieved.

You could use an <iframe> and target the <iframe> with different galleries via links to the corresponding 'index.hml' pages.

Otherwise, you could embed a gallery in a container and, using the Juicebox-Pro API, you could switch galleries using JavaScript and the showGallery() method.

Either method would require knowledge of HTML and/or JavaScript.

You may also like to take a look at the Embedding Multiple Galleries section of the Juicebox Embedding Guide.

A further solution might be to create a multiple-gallery album using jAlbum and the Juicebox Skin.
When using jAlbum and the Juicebox skin, you can drag and drop a complete folder structure into jAlbum's main window and click 'Make Album'.
The resulting album will have a separate Juicebox gallery for each and every folder/subfolder in your input structure and all the galleries will be linked together via a JavaScript navigation tree. On clicking a link for a gallery, the current gallery is replaced with the newly selected one.
Here is a sample album created by jAlbum and the Juicebox Skin.