If you plan to embed multiple galleries on a single page, you can do the following:
(1) Create your galleries and keep each one in its own folder.
(2) Upload the complete gallery folders (not just the contents) to your web server.
(3) Embed each gallery in your web page using the baseUrl method documented here.

Here are a few tips:

• It does not matter where on your web server you upload your gallery folders to as long as the two paths within the baseUrl embedding code (the path to the 'juicebox.js' file and the baseUrl itself) are correct.

• Each gallery must be embedded in a <div> with a unique 'id'.

• It is necessary to load the 'juicebox.js' file only once per page (not once per gallery).

For example, if you were to embed two galleries on a single page, the embedding code for the two galleries might look something like this.

<script src="http://www.example.com/gallery1/jbcore/juicebox.js"></script>

<script>
  new juicebox({
    baseUrl: 'http://www.example.com/gallery1/',
    containerId: 'juicebox-container1',
    galleryWidth : '800',
    galleryHeight : '600',
    backgroundColor: '#222222'
  });
  </script>
<div id="juicebox-container1"></div>

<script>
  new juicebox({
    baseUrl: 'http://www.example.com/gallery2/',
    containerId: 'juicebox-container2',
    galleryWidth : '800',
    galleryHeight : '600',
    backgroundColor: '#222222'
  });
  </script>
<div id="juicebox-container2"></div>

If you are embedding multiple galleries on different pages (i.e. only one gallery per page, then you can follow the standard embedding instructions here or the baseUrl method. Either will work equally well.
CSS (Cascading Style Sheets) is a method of styling web pages. It is not possible to embed a gallery 'in another CSS'. Do you perhaps mean a CMS (Content Management System) such as WordPress, Joomla or Drupal? If so, you can embed Juicebox galleries in any web page in the same way.